1
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Ji X, Wu Q, Cao X, Liu S, Zhang J, Chen S, Shan J, Zhang Y, Li B, Zhao H. Helicobacter pylori East Asian type CagA hijacks more SHIP2 by its EPIYA-D motif to potentiate the oncogenicity. Virulence 2024; 15:2375549. [PMID: 38982595 PMCID: PMC11238919 DOI: 10.1080/21505594.2024.2375549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2024] Open
Abstract
CagA is a significant oncogenic factor injected into host cells by Helicobacter pylori, which is divided into two subtypes: East Asian type (CagAE), characterized by the EPIYA-D motif, and western type (CagAW), harboring the EPIYA-C motif. CagAE has been reported to have higher carcinogenicity than CagAW, although the underlying reason is not fully understood. SHIP2 is an intracellular phosphatase that can be recruited by CagA to perturb the homeostasis of intracellular signaling pathways. In this study, we found that SHIP2 contributes to the higher oncogenicity of CagAE. Co-Immunoprecipitation and Pull-down assays showed that CagAE bind more SHIP2 than CagAW. Immunofluorescence staining showed that a higher amount of SHIP2 recruited by CagAE to the plasma membrane catalyzes the conversion of PI(3,4,5)P3 into PI(3,4)P2. This alteration causes higher activation of Akt signaling, which results in enhanced IL-8 secretion, migration, and invasion of the infected cells. SPR analysis showed that this stronger interaction between CagAE and SHIP2 stems from the higher affinity between the EPIYA-D motif of CagAE and the SH2 domain of SHIP2. Structural analysis revealed the crucial role of the Phe residue at the Y + 5 position in EPIYA-D. After mutating Phe of CagAE into Asp (the corresponding residue in the EPIYA-C motif) or Ala, the activation of downstream Akt signaling was reduced and the malignant transformation of infected cells was alleviated. These findings revealed that CagAE hijacks SHIP2 through its EPIYA-D motif to enhance its carcinogenicity, which provides a better understanding of the higher oncogenic risk of H. pylori CagAE.
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Affiliation(s)
- Xiaofei Ji
- School of Basic Medical Sciences, Binzhou Medical University, Yantai, Shandong, China
| | - Qianwen Wu
- The Second School of Clinical Medicine, Binzhou Medical University, Yantai, Shandong, China
| | - Xinying Cao
- School of Basic Medical Sciences, Binzhou Medical University, Yantai, Shandong, China
| | - Shuzhen Liu
- School of Basic Medical Sciences, Binzhou Medical University, Yantai, Shandong, China
| | - Jianhui Zhang
- School of Basic Medical Sciences, Binzhou Medical University, Yantai, Shandong, China
| | - Si Chen
- School of Basic Medical Sciences, Binzhou Medical University, Yantai, Shandong, China
| | - Jiangfan Shan
- School of Basic Medical Sciences, Binzhou Medical University, Yantai, Shandong, China
| | - Ying Zhang
- The Second School of Clinical Medicine, Binzhou Medical University, Yantai, Shandong, China
| | - Boqing Li
- School of Basic Medical Sciences, Binzhou Medical University, Yantai, Shandong, China
| | - Huilin Zhao
- School of Basic Medical Sciences, Binzhou Medical University, Yantai, Shandong, China
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2
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Yu J, Yan C, Paul T, Brewer L, Tsutakawa SE, Tsai CL, Hamdan SM, Tainer JA, Ivanov I. Molecular architecture and functional dynamics of the pre-incision complex in nucleotide excision repair. Nat Commun 2024; 15:8511. [PMID: 39353945 PMCID: PMC11445577 DOI: 10.1038/s41467-024-52860-y] [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] [Received: 03/27/2024] [Accepted: 09/19/2024] [Indexed: 10/04/2024] Open
Abstract
Nucleotide excision repair (NER) is vital for genome integrity. Yet, our understanding of the complex NER protein machinery remains incomplete. Combining cryo-EM and XL-MS data with AlphaFold2 predictions, we build an integrative model of the NER pre-incision complex(PInC). Here TFIIH serves as a molecular ruler, defining the DNA bubble size and precisely positioning the XPG and XPF nucleases for incision. Using simulations and graph theoretical analyses, we unveil PInC's assembly, global motions, and partitioning into dynamic communities. Remarkably, XPG caps XPD's DNA-binding groove and bridges both junctions of the DNA bubble, suggesting a novel coordination mechanism of PInC's dual incision. XPA rigging interlaces XPF/ERCC1 with RPA, XPD, XPB, and 5' ssDNA, exposing XPA's crucial role in licensing the XPF/ERCC1 incision. Mapping disease mutations onto our models reveals clustering into distinct mechanistic classes, elucidating xeroderma pigmentosum and Cockayne syndrome disease etiology.
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Affiliation(s)
- Jina Yu
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
- Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
| | - Chunli Yan
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
- Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
| | - Tanmoy Paul
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
- Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
| | - Lucas Brewer
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
- Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
| | - Susan E Tsutakawa
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Chi-Lin Tsai
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Samir M Hamdan
- Bioscience Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - John A Tainer
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Ivaylo Ivanov
- Department of Chemistry, Georgia State University, Atlanta, GA, USA.
- Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA.
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3
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Zheng X, Hu Z, Gao S, Li Z, Chen J, Zhang G, Kong N, Sun J, Liu W. One-pot assay using a target-driven split aptamer recognition and assembly strategy for convenient and rapid detection of gliotoxin. Food Chem 2024; 454:139738. [PMID: 38820643 DOI: 10.1016/j.foodchem.2024.139738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 05/16/2024] [Accepted: 05/17/2024] [Indexed: 06/02/2024]
Abstract
An aptamer targeting gliotoxin (GTX) was optimized to increase the binding affinity by approximately 20 times and achieve higher structural stability and targeting specificity. Molecular dynamics simulations were used to explore the molecular mechanism and key action sites underlying the recognition of GTX by the optimized aptamer. Subsequently, the optimized aptamer was split into two fragments and a convenient and rapid one-pot assay for GTX detection was successfully established using a target-driven split aptamer recognition and assembly strategy. The method exhibited a good linear range of 0.128 nM to 2 μM, a low detection limit of 0.07 nM, and excellent selectivity for GTX. Furthermore, the method had good accuracy and stability in real sample analysis. Therefore, the developed one-pot method provides a reliable, convenient, and cost-effective approach for the widespread application of GTX detection.
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Affiliation(s)
- Xin Zheng
- Department of Laboratory Medicine, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Zunqi Hu
- Department of General Surgery, Changzheng Hospital, Naval Medical University, Shanghai 200003, China
| | - Shunxiang Gao
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China; National Clinical Research Center for Eye Diseases, Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai 200080, China.
| | - Zhen Li
- Department of Laboratory Medicine, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Jia Chen
- Department of Laboratory Medicine, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Guanyi Zhang
- Department of Laboratory Medicine, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Nana Kong
- Department of Laboratory Medicine, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Jianguo Sun
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Shanghai Medical College, Fudan University, Shanghai 200031, China
| | - Weiwei Liu
- Department of Laboratory Medicine, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China.
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4
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Wang YP, Eriksson LA, Zhang RB. Mechanism of Dual-Site Recognition in a Classic DNA Aptamer. J Chem Inf Model 2024. [PMID: 39327929 DOI: 10.1021/acs.jcim.4c01389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2024]
Abstract
Nucleic acid aptamers possess unique advantages in specific recognition. However, the lack of in-depth investigation into their dynamic recognition mechanisms has restricted their rational design and potential applications in fields such as biosensing and targeted therapy. We herein utilized enhanced sampling molecular dynamics to address affinities of adenosine monophosphate (AMP) to the dual binding sites in the DNA aptamer, focusing on the dynamic recognition mechanism and pathways. The present results indicate that in addition to the widely known intermolecular interactions, inequivalence of chemical environments of the two binding sites leads to slightly higher stability of AMP binding to the site proximal to the aptamer terminus. In the presence of two AMPs captured by the two sites, each binding free energy is enhanced. In particular, an additional hydrogen bond of AMP to A10 is introduced in the dual-site binding complex, which increases the binding energy from -4.25 ± 0.47 to -9.48 ± 0.33 kcal mol-1 in the site close to the loop. For the dual-site recognition process, the free energy landscape and minimum free energy pathway calculations elucidate the crucial role of electrostatic interactions between the AMP phosphate groups and Na+ ions in positively cooperative binding mechanisms.
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Affiliation(s)
- Yun-Peng Wang
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, South Street No. 5, Zhongguancun, Haidian District, Beijing 100081, China
| | - Leif A Eriksson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan 7b, Göteborg 405 30, Sweden
| | - Ru-Bo Zhang
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, South Street No. 5, Zhongguancun, Haidian District, Beijing 100081, China
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5
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Wondimagegnhu B, Ma W, Paul T, Liao TW, Lee C, Sanford S, Opresko P, Myong S. The molecular mechanism for TERRA recruitment and annealing to telomeres. Nucleic Acids Res 2024; 52:10490-10503. [PMID: 39189448 PMCID: PMC11417404 DOI: 10.1093/nar/gkae732] [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] [Received: 04/18/2024] [Accepted: 08/16/2024] [Indexed: 08/28/2024] Open
Abstract
Telomeric repeat containing RNA (TERRA) is a noncoding RNA that is transcribed from telomeres. Previous study showed that TERRA trans anneals by invading into the telomeric duplex to form an R-loop in mammalian cells. Here, we elucidate the molecular mechanism underlying TERRA recruitment and invasion into telomeres in the context of shelterin proteins, RAD51 and RNase H using single molecule (sm) assays. We demonstrate that TERRA trans annealing into telomeric DNA exhibits dynamic movement that is stabilized by TRF2. TERRA annealing to the telomeric duplex results in the formation of a stable triplex structure which differs from a conventional R-loop. We identified that the presence of a sub-telomeric DNA and a telomeric overhang in the form of a G-quadruplex significantly enhances TERRA annealing to telomeric duplex. We also demonstrate that RAD51-TERRA complex invades telomere duplex more efficiently than TERRA alone. Additionally, TRF2 increases TERRA affinity to telomeric duplex and protects it from RNase H digestion. In contrast, TRF1 represses TERRA annealing to telomeric duplex and fails to provide protection against RNase H digestion. Our findings provide an in-depth molecular mechanism underpinning TERRA recruitment and annealing to the telomere.
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Affiliation(s)
- Bersabel Wondimagegnhu
- Program in Cell, Molecular, Developmental Biology and Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Wen Ma
- Department of Physics, The University of Vermont, Burlington, VT 05405, USA
| | - Tapas Paul
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ting-Wei Liao
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Chun Ying Lee
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Samantha Sanford
- Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, Pittsburgh, PA 15261, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
| | - Patricia L Opresko
- Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, Pittsburgh, PA 15261, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
| | - Sua Myong
- Program in Cell, Molecular, Developmental Biology and Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
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6
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Ros-Pardo D, Gómez-Puertas P, Marcos-Alcalde Í. STAG2-RAD21 complex: A unidirectional DNA ratchet mechanism in loop extrusion. Int J Biol Macromol 2024; 276:133822. [PMID: 39002918 DOI: 10.1016/j.ijbiomac.2024.133822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 07/08/2024] [Accepted: 07/09/2024] [Indexed: 07/15/2024]
Abstract
DNA loop extrusion plays a key role in the regulation of gene expression and the structural arrangement of chromatin. Most existing mechanistic models of loop extrusion depend on some type of ratchet mechanism, which should permit the elongation of loops while preventing their collapse, by enabling DNA to move in only one direction. STAG2 is already known to exert a role as DNA anchor, but the available structural data suggest a possible role in unidirectional DNA motion. In this work, a computational simulation framework was constructed to evaluate whether STAG2 could enforce such unidirectional displacement of a DNA double helix. The results reveal that STAG2 V-shape allows DNA sliding in one direction, but blocks opposite DNA movement via a linear ratchet mechanism. Furthermore, these results suggest that RAD21 binding to STAG2 controls its flexibility by narrowing the opening of its V-shape, which otherwise remains widely open in absence of RAD21. Therefore, in the proposed model, in addition to its already described role as a DNA anchor, the STAG2-RAD21 complex would be part of a ratchet mechanism capable of exerting directional selectivity on DNA sliding during loop extrusion. The identification of the molecular basis of the ratchet mechanism of loop extrusion is a critical step in unraveling new insights into a broad spectrum of chromatin activities and their implications for the mechanisms of chromatin-related diseases.
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Affiliation(s)
- David Ros-Pardo
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, CL Nicolás Cabrera, 1, 28049 Madrid, Spain
| | - Paulino Gómez-Puertas
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, CL Nicolás Cabrera, 1, 28049 Madrid, Spain.
| | - Íñigo Marcos-Alcalde
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, CL Nicolás Cabrera, 1, 28049 Madrid, Spain
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7
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Bayıl I, Sarowar Hossain M, Tamanna S, Jamir Uddin M, Mashood Ahamed FM, Jardan YAB, Bourhia M, Taskin Tok T. Aptamer biosensor design for the detection of endocrine-disrupting chemicals small organic molecules using novel bioinformatics methods. J Mol Graph Model 2024; 131:108785. [PMID: 38820705 DOI: 10.1016/j.jmgm.2024.108785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/25/2024] [Accepted: 04/29/2024] [Indexed: 06/02/2024]
Abstract
Endocrine-disrupting chemicals (EDCs) are substances that can disrupt the normal functioning of hormones.Using aptamers, which are biological recognition elements, biosensors can quickly and accurately detect EDCs in environmental samples. However, the elucidation of aptamer structures by conventional methods is highly challenging due to their complexity. This has led to the development of three-dimensional aptamer structures based on different models and techniques. To do this, we developed a way to predict the 3D structures of the SS DNA needed for this sequence by starting with an aptamer sequence that has biosensor properties specific to bisphenol-A (BPA), one of the chemicals found in water samples that can interfere with hormones. In addition, we will elucidate the intermolecular mechanisms and binding affinity between aptamers and endocrine disruptors using bioinformatics techniques such as molecular docking, molecular dynamics simulation, and binding energies. The outcomes of our study are to compare modeling programs and force fields to see how reliable they are and how well they agree with results found in the existing literature, to understand the intermolecular mechanisms and affinity of aptamer-based biosensors, and to find a new way to make aptamers that takes less time and costs less.
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Affiliation(s)
- Imren Bayıl
- Department of Bioinformatics and Computational Biology, Gaziantep University, Turkey.
| | - Md Sarowar Hossain
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Birulia 1216, Ashulia, Dhaka, Bangladesh; Faculty of Pharmaceutical Science, Assam Down Town University, Guwahati, Assam, India.
| | - Sonia Tamanna
- Department of Biochemistry and Molecular Biology, University of Dhaka. Dhaka-1000, Bangladesh.
| | - Md Jamir Uddin
- Department of Chemistry, Hajee Mohammad Danesh Science and Technology University, Dinajpur, 5200, Bangladesh.
| | - F M Mashood Ahamed
- PG and Research Department of Chemistry, Jamal Mohamed College (Autonomous), Tiruchirappalli, 620020, India; Affiliated to Bharathidasan University, Tamilnadu, India.
| | - Yousef A Bin Jardan
- Department of Pharmaceutics, College of Pharmacy, King Saud University, P.O. Box 11451, Riyadh, Saudi Arabia.
| | - Mohammed Bourhia
- Department of Chemistry and Biochemistry, Faculty of Medicine and Pharmacy, Ibn Zohr University, Laayoune 70000, Morocco.
| | - Tugba Taskin Tok
- Faculty of Science, Department of Chemistry, Gaziantep University, Turkey.
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8
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Mou X, Liu K, He L, Li S. Mechanical response of double-stranded DNA: Bend, twist, and overwind. J Chem Phys 2024; 161:085102. [PMID: 39177087 DOI: 10.1063/5.0216585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 08/09/2024] [Indexed: 08/24/2024] Open
Abstract
We employed all-atom molecular dynamics simulations to explore the mechanical response of bending, twisting, and overwinding for double-stranded DNA (dsDNA). We analyzed the bending and twisting deformations, as well as their stiffnesses, using the tilt, roll, and twist modes under stretching force. Findings indicate that the roll and twist angles vary linearly with the stretching force but show opposite trends. The tilt, roll, and twist elastic moduli are considered constants, while the coupling between roll and twist modes slightly decreases under stretching force. The effect of the stretching force on the roll and twist modes, including both their deformations and elasticities, exhibits sequence-dependence, with symmetry around the base pair step. Furthermore, we examined the overwinding path and mechanism of dsDNA from the perspective of the stiffness matrix, based on the tilt, roll, and twist modes. The correlations among tilt, roll, and twist angles imply an alternative overwinding pathway via twist-roll coupling when dsDNA is stretched, wherein entropic contribution prevails.
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Affiliation(s)
- Xuankang Mou
- Department of Physics, Wenzhou University, Wenzhou, Zhejiang 325035, China
| | - Kai Liu
- Department of Physics, Wenzhou University, Wenzhou, Zhejiang 325035, China
| | - Linli He
- Department of Physics, Wenzhou University, Wenzhou, Zhejiang 325035, China
| | - Shiben Li
- Department of Physics, Wenzhou University, Wenzhou, Zhejiang 325035, China
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9
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Arad E, Levi T, Yosefi G, Kass I, Cohen-Erez I, Azoulay Z, Bitton R, Jelinek R, Rapaport H. A Matter of Charge: Electrostatically Tuned Coassembly of Amphiphilic Peptides. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2404324. [PMID: 39155426 DOI: 10.1002/smll.202404324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 08/04/2024] [Indexed: 08/20/2024]
Abstract
Coassembly of peptide biomaterials offers a compelling avenue to broaden the spectrum of hierarchically ordered supramolecular nanoscale structures that may be relevant for biomedical and biotechnological applications. In this work coassemblies of amphiphilic and oppositely charged, anionic and cationic, β-sheet peptides are studied, which may give rise to a diverse range of coassembled forms. Mixtures of the peptides show significantly lower critical coassembly concentration (CCC) values compared to those of the individual pure peptides. Intriguingly, the highest formation of coassembled fibrils is found to require excess of the cationic peptide whereas equimolar mixtures of the peptides exhibited the maximum folding into β-sheet structures. Mixtures of the peptides coassembled sequentially from solutions at concentrations surpassing each peptide's intrinsic critical assembly concentration (CAC), are also found to require a higher portion of the cationic peptide to stabilize hydrogels. This study illuminates a systematic investigation of oppositely charged β-sheet peptides over a range of concentrations, in solutions and in hydrogels. The results may be relevant to the fundamental understanding of such intricate charge-driven assembly systems and to the formulation of peptide-based nanostructures with diverse functionalities.
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Affiliation(s)
- Elad Arad
- Ilse Katz Institute (IKI) for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel
- Department of Chemical Engineering, Columbia University in the City of New York, New York, NY, 10027, USA
| | - Topaz Levi
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel
| | - Gal Yosefi
- Department of Chemical Engineering, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel
| | - Itamar Kass
- Ilse Katz Institute (IKI) for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel
| | - Ifat Cohen-Erez
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel
| | - Ziv Azoulay
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel
| | - Ronit Bitton
- Ilse Katz Institute (IKI) for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel
- Department of Chemical Engineering, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel
| | - Raz Jelinek
- Ilse Katz Institute (IKI) for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel
| | - Hanna Rapaport
- Ilse Katz Institute (IKI) for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel
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10
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Choi SR, Lee J, Seo YJ, Jin HS, Ahn HB, Go Y, Kim NK, Ryu KS, Lee JH. Molecular basis of facilitated target search and sequence discrimination of TALE homeodomain transcription factor Meis1. Nat Commun 2024; 15:6984. [PMID: 39143123 PMCID: PMC11325038 DOI: 10.1038/s41467-024-51297-7] [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] [Received: 02/22/2023] [Accepted: 08/05/2024] [Indexed: 08/16/2024] Open
Abstract
Transcription factors specifically bind to their consensus sequence motifs and regulate transcription efficiency. Transcription factors are also able to non-specifically contact the phosphate backbone of DNA through electrostatic interaction. The homeodomain of Meis1 TALE human transcription factor (Meis1-HD) recognizes its target DNA sequences via two DNA contact regions, the L1-α1 region and the α3 helix (specific binding mode). This study demonstrates that the non-specific binding mode of Meis1-HD is the energetically favored process during DNA binding, achieved by the interaction of the L1-α1 region with the phosphate backbone. An NMR dynamics study suggests that non-specific binding might set up an intermediate structure which can then rapidly and easily find the consensus region on a long section of genomic DNA in a facilitated binding process. Structural analysis using NMR and molecular dynamics shows that key structural distortions in the Meis1-HD-DNA complex are induced by various single nucleotide mutations in the consensus sequence, resulting in decreased DNA binding affinity. Collectively, our results elucidate the detailed molecular mechanism of how Meis1-HD recognizes single nucleotide mutations within its consensus sequence: (i) through the conformational features of the α3 helix; and (ii) by the dynamic features (rigid or flexible) of the L1 loop and the α3 helix. These findings enhance our understanding of how single nucleotide mutations in transcription factor consensus sequences lead to dysfunctional transcription and, ultimately, human disease.
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Affiliation(s)
- Seo-Ree Choi
- Department of Chemistry and RINS, Gyeongsang National University, Jinju, Gyeongsangnam-do, 52828, Republic of Korea
- Advanced Analysis Data Center, Korea Institute of Science and Technology, Seoul, 02456, Republic of Korea
| | - Juyong Lee
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, and College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea.
- Research Institute of Pharmaceutical Science, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea.
- Arontier Co., Seoul, 06735, Republic of Korea.
| | - Yeo-Jin Seo
- Department of Chemistry and RINS, Gyeongsang National University, Jinju, Gyeongsangnam-do, 52828, Republic of Korea
| | - Ho-Seong Jin
- Department of Chemistry and RINS, Gyeongsang National University, Jinju, Gyeongsangnam-do, 52828, Republic of Korea
| | - Hye-Bin Ahn
- Department of Chemistry and RINS, Gyeongsang National University, Jinju, Gyeongsangnam-do, 52828, Republic of Korea
| | - Youyeon Go
- Department of Chemistry and RINS, Gyeongsang National University, Jinju, Gyeongsangnam-do, 52828, Republic of Korea
| | - Nak-Kyoon Kim
- Advanced Analysis Data Center, Korea Institute of Science and Technology, Seoul, 02456, Republic of Korea
| | - Kyoung-Seok Ryu
- Protein Structure Research Team, Korea Basic Science Institute, Cheongju, Chungcheongbuk-do, 28119, Republic of Korea
| | - Joon-Hwa Lee
- Department of Chemistry and RINS, Gyeongsang National University, Jinju, Gyeongsangnam-do, 52828, Republic of Korea
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11
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Takaba K, Friedman AJ, Cavender CE, Behara PK, Pulido I, Henry MM, MacDermott-Opeskin H, Iacovella CR, Nagle AM, Payne AM, Shirts MR, Mobley DL, Chodera JD, Wang Y. Machine-learned molecular mechanics force fields from large-scale quantum chemical data. Chem Sci 2024; 15:12861-12878. [PMID: 39148808 PMCID: PMC11322960 DOI: 10.1039/d4sc00690a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 06/17/2024] [Indexed: 08/17/2024] Open
Abstract
The development of reliable and extensible molecular mechanics (MM) force fields-fast, empirical models characterizing the potential energy surface of molecular systems-is indispensable for biomolecular simulation and computer-aided drug design. Here, we introduce a generalized and extensible machine-learned MM force field, espaloma-0.3, and an end-to-end differentiable framework using graph neural networks to overcome the limitations of traditional rule-based methods. Trained in a single GPU-day to fit a large and diverse quantum chemical dataset of over 1.1 M energy and force calculations, espaloma-0.3 reproduces quantum chemical energetic properties of chemical domains highly relevant to drug discovery, including small molecules, peptides, and nucleic acids. Moreover, this force field maintains the quantum chemical energy-minimized geometries of small molecules and preserves the condensed phase properties of peptides and folded proteins, self-consistently parametrizing proteins and ligands to produce stable simulations leading to highly accurate predictions of binding free energies. This methodology demonstrates significant promise as a path forward for systematically building more accurate force fields that are easily extensible to new chemical domains of interest.
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Affiliation(s)
- Kenichiro Takaba
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York NY 10065 USA
- Pharmaceuticals Research Center, Advanced Drug Discovery, Asahi Kasei Pharma Corporation Shizuoka 410-2321 Japan
| | - Anika J Friedman
- Department of Chemical and Biological Engineering, University of Colorado Boulder Boulder CO 80309 USA
| | - Chapin E Cavender
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| | - Pavan Kumar Behara
- Center for Neurotherapeutics, Department of Pathology and Laboratory Medicine, University of California Irvine CA 92697 USA
| | - Iván Pulido
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York NY 10065 USA
| | - Michael M Henry
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York NY 10065 USA
| | | | - Christopher R Iacovella
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York NY 10065 USA
| | - Arnav M Nagle
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York NY 10065 USA
- Department of Bioengineering, University of California, Berkeley Berkeley CA 94720 USA
| | - Alexander Matthew Payne
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York NY 10065 USA
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center New York 10065 USA
| | - Michael R Shirts
- Department of Chemical and Biological Engineering, University of Colorado Boulder Boulder CO 80309 USA
| | - David L Mobley
- Department of Pharmaceutical Sciences, University of California Irvine California 92697 USA
| | - John D Chodera
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York NY 10065 USA
| | - Yuanqing Wang
- Simons Center for Computational Physical Chemistry and Center for Data Science, New York University New York NY 10004 USA
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York NY 10065 USA
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12
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Ukladov EO, Tyugashev TE, Kuznetsov NA. Computational Modeling Study of the Molecular Basis of dNTP Selectivity in Human Terminal Deoxynucleotidyltransferase. Biomolecules 2024; 14:961. [PMID: 39199349 PMCID: PMC11352444 DOI: 10.3390/biom14080961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Revised: 08/03/2024] [Accepted: 08/05/2024] [Indexed: 09/01/2024] Open
Abstract
Human terminal deoxynucleotidyl transferase (TdT) can catalyze template-independent DNA synthesis during the V(D)J recombination and DNA repair through nonhomologous end joining. The capacity for template-independent random addition of nucleotides to single-stranded DNA makes this polymerase useful in various molecular biological applications involving sequential stepwise synthesis of oligonucleotides using modified dNTP. Nonetheless, a serious limitation to the applications of this enzyme is strong selectivity of human TdT toward dNTPs in the order dGTP > dTTP ≈ dATP > dCTP. This study involved molecular dynamics to simulate a potential impact of amino acid substitutions on the enzyme's selectivity toward dNTPs. It was found that the formation of stable hydrogen bonds between a nitrogenous base and amino acid residues at positions 395 and 456 is crucial for the preferences for dNTPs. A set of single-substitution and double-substitution mutants at these positions was analyzed by molecular dynamics simulations. The data revealed two TdT mutants-containing either substitution D395N or substitutions D395N+E456N-that possess substantially equalized selectivity toward various dNTPs as compared to the wild-type enzyme. These results will enable rational design of TdT-like enzymes with equalized dNTP selectivity for biotechnological applications.
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Affiliation(s)
- Egor O. Ukladov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia; (E.O.U.); (T.E.T.)
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Timofey E. Tyugashev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia; (E.O.U.); (T.E.T.)
| | - Nikita A. Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia; (E.O.U.); (T.E.T.)
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
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13
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Mazzini S, Borgonovo G, Princiotto S, Artali R, Musso L, Aviñó A, Eritja R, Gargallo R, Dallavalle S. Quadruplex-duplex junction in LTR-III: A molecular insight into the complexes with BMH-21, namitecan and doxorubicin. PLoS One 2024; 19:e0306239. [PMID: 39046961 PMCID: PMC11268700 DOI: 10.1371/journal.pone.0306239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 06/13/2024] [Indexed: 07/27/2024] Open
Abstract
Quadruplex-Duplex (Q-D) junctions are unique structural motifs garnering increasing interest as drug targets, due to their frequent occurrence in genomic sequences. The viral HIV LTR-III sequence was chosen as a Q-D junction model to study the affinity of the selected compounds BMH-21, namitecan (ST-1968), and doxorubicin (DOXO), all containing a planar polycyclic aromatic moiety, linked to either one short aminoalkyl or an aminoglycosyl group. A multidisciplinary approach that combines NMR spectroscopy, molecular modelling, circular dichroism (CD) and fluorescence spectroscopy was employed. The studied ligands induced moderate but clear stabilization to the Q-D junction by interacting with the interfacial tetrad. DOXO was found to be the best Q-D junction binder. Interestingly, the removal of the aminoglycosyl group significantly changed the pattern of the interactions, indicating that highly polar substituents have a stronger affinity with the exposed regions of the Q-D junction, particularly at the level of the interfacial tetrad.
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Affiliation(s)
- Stefania Mazzini
- Department of Food, Environmental and Nutritional Sciences (DEFENS), University of Milan, Milan, Italy
| | - Gigliola Borgonovo
- Department of Food, Environmental and Nutritional Sciences (DEFENS), University of Milan, Milan, Italy
| | - Salvatore Princiotto
- Department of Food, Environmental and Nutritional Sciences (DEFENS), University of Milan, Milan, Italy
| | - Roberto Artali
- Scientia Advice di Roberto Artali, Cesano Maderno (MB), Italy
| | - Loana Musso
- Department of Food, Environmental and Nutritional Sciences (DEFENS), University of Milan, Milan, Italy
| | - Anna Aviñó
- Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), ISCIII, Barcelona, Spain
| | - Ramon Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), ISCIII, Barcelona, Spain
| | - Raimundo Gargallo
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Barcelona, Spain
| | - Sabrina Dallavalle
- Department of Food, Environmental and Nutritional Sciences (DEFENS), University of Milan, Milan, Italy
- National Institute of Fundamental Studies, Kandy, Sri Lanka
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14
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Liu T, Simine L. DeltaGzip: Computing Biopolymer-Ligand Binding Affinity via Kolmogorov Complexity and Lossless Compression. J Chem Inf Model 2024; 64:5617-5623. [PMID: 38980667 DOI: 10.1021/acs.jcim.4c00461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
The design of biosequences for biosensing and therapeutics is a challenging multistep search and optimization task. In principle, computational modeling may speed up the design process by virtual screening of sequences based on their binding affinities to target molecules. However, in practice, existing machine-learned models trained to predict binding affinities lack the flexibility with respect to reaction conditions, and molecular dynamics simulations that can incorporate reaction conditions suffer from high computational costs. Here, we describe a computational approach called DeltaGzip that evaluates the free energy of binding in biopolymer-ligand complexes from ultrashort equilibrium molecular dynamics simulations. The entropy of binding is evaluated using the Kolmogorov complexity definition of entropy and approximated using a lossless compression algorithm, Gzip. We benchmark the method on a well-studied data set of protein-ligand complexes comparing the predictions of DeltaGzip to the free energies of binding obtained using Jarzynski equality and experimental measurements.
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Affiliation(s)
- Tao Liu
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Lena Simine
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
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15
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Slavkovic S, Shoara AA, Kaiyum YA, Churcher ZR, Liu T, Simine L, Johnson PE. Amodiaquine Nonspecifically Binds Double Stranded and Three-Way Junction DNA Structures. Chembiochem 2024; 25:e202400116. [PMID: 38668388 DOI: 10.1002/cbic.202400116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 04/20/2024] [Indexed: 06/18/2024]
Abstract
The 4-aminoquinoline class of compounds includes the important antimalarial compounds amodiaquine and chloroquine. Despite their medicinal importance, the mode of action of these compounds is poorly understood. In a previous study we observed these compounds, as well as quinine and mefloquine, tightly bind the DNA cocaine-binding aptamer. Here, we further explore the range of nucleic acid structures bound by these compounds. To gauge a wide range of binding affinities, we used isothermal titration calorimetry to explore high affinity binding (nM to tens of μM) and NMR spectroscopy to assay weak binding biding in the hundreds of micromolar range. We find that amodiaquine tightly binds all double stranded DNA structures explored. Mefloquine binds double stranded DNA duplex molecules tightly and weakly associates with a three-way junction DNA construct. Quinine and chloroquine only weakly bind duplex DNA but do not tightly bind any of the DNA constructs explored. A simulation of the free energy of binding of these ligands to the Dickerson-Drew dodecamer resulted in an excellent agreement between the simulated and experimental free energy. These results provide new insight into the DNA binding of clinically important antimalarial compounds and may play a role in future development of new antimalarials.
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Affiliation(s)
- Sladjana Slavkovic
- Department of Chemistry, York University, 4700 Keele St., Toronto, Ontario, Canada, M3J 1P3
| | - Aron A Shoara
- Department of Chemistry, York University, 4700 Keele St., Toronto, Ontario, Canada, M3J 1P3
| | - Yunus A Kaiyum
- Department of Chemistry, York University, 4700 Keele St., Toronto, Ontario, Canada, M3J 1P3
| | - Zachary R Churcher
- Department of Chemistry, York University, 4700 Keele St., Toronto, Ontario, Canada, M3J 1P3
| | - Tao Liu
- Department of Chemistry, McGill University, Montreal, Quebec, Canada, H3A 0B8
| | - Lena Simine
- Department of Chemistry, McGill University, Montreal, Quebec, Canada, H3A 0B8
| | - Philip E Johnson
- Department of Chemistry, York University, 4700 Keele St., Toronto, Ontario, Canada, M3J 1P3
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16
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Tarek Ibrahim M, Wait E, Ren P. Quantum Mechanics Characterization of Non-Covalent Interaction in Nucleotide Fragments. Molecules 2024; 29:3258. [PMID: 39064837 PMCID: PMC11279843 DOI: 10.3390/molecules29143258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 07/03/2024] [Accepted: 07/06/2024] [Indexed: 07/28/2024] Open
Abstract
Accurate calculation of non-covalent interaction energies in nucleotides is crucial for understanding the driving forces governing nucleic acid structure and function, as well as developing advanced molecular mechanics forcefields or machine learning potentials tailored to nucleic acids. Here, we dissect the nucleotides' structure into three main constituents: nucleobases (A, G, C, T, and U), sugar moieties (ribose and deoxyribose), and phosphate group. The interactions among these fragments and between fragments and water were analyzed. Different quantum mechanical methods were compared for their accuracy in capturing the interaction energy. The non-covalent interaction energy was decomposed into electrostatics, exchange-repulsion, dispersion, and induction using two ab initio methods: Symmetry-Adapted Perturbation Theory (SAPT) and Absolutely Localized Molecular Orbitals (ALMO). These calculations provide a benchmark for different QM methods, in addition to providing a valuable understanding of the roles of various intermolecular forces in hydrogen bonding and aromatic stacking. With SAPT, a higher theory level and/or larger basis set did not necessarily give more accuracy. It is hard to know which combination would be best for a given system. In contrast, ALMO EDA2 did not show dependence on theory level or basis set; additionally, it is faster.
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Affiliation(s)
- Mayar Tarek Ibrahim
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA;
| | - Elizabeth Wait
- Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, TX 78712, USA;
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA;
- Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, TX 78712, USA;
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17
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Cristofaro S, Querciagrossa L, Soprani L, Fraccia TP, Bellini T, Berardi R, Arcioni A, Zannoni C, Muccioli L, Orlandi S. Simulating the Lyotropic Phase Behavior of a Partially Self-Complementary DNA Tetramer. Biomacromolecules 2024; 25:3920-3929. [PMID: 38826125 DOI: 10.1021/acs.biomac.3c01435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
DNA oligomers in solution have been found to develop liquid crystal phases via a hierarchical process that involves Watson-Crick base pairing, supramolecular assembly into columns of duplexes, and long-range ordering. The multiscale nature of this phenomenon makes it difficult to quantitatively describe and assess the importance of the various contributions, particularly for very short strands. We performed molecular dynamics simulations based on the coarse-grained oxDNA model, aiming to depict all of the assembly processes involved and the phase behavior of solutions of the DNA GCCG tetramers. We find good quantitative matching to experimental data at both levels of molecular association (thermal melting) and collective ordering (phase diagram). We characterize the isotropic state and the low-density nematic and high-density columnar liquid crystal phases in terms of molecular order, size of aggregates, and structure, together with their effects on diffusivity processes. We observe a cooperative aggregation mechanism in which the formation of dimers is less thermodynamically favored than the formation of longer aggregates.
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Affiliation(s)
- Silvia Cristofaro
- Dipartimento di Chimica Industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, Bologna 40136, Italy
| | - Lara Querciagrossa
- CINECA, Via Magnanelli 6/3, Casalecchio di Reno 40033, Italy
- Dipartimento di Chimica Industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, Bologna 40136, Italy
| | - Lorenzo Soprani
- Dipartimento di Chimica Industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, Bologna 40136, Italy
| | - Tommaso P Fraccia
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università di Milano, Via Balzaretti 9, Milano 20133, Italy
| | - Tommaso Bellini
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università di Milano, Via Vanvitelli 32, Milano 20129, Italy
| | - Roberto Berardi
- Dipartimento di Chimica Industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, Bologna 40136, Italy
| | - Alberto Arcioni
- Dipartimento di Chimica Industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, Bologna 40136, Italy
| | - Claudio Zannoni
- Dipartimento di Chimica Industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, Bologna 40136, Italy
| | - Luca Muccioli
- Dipartimento di Chimica Industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, Bologna 40136, Italy
| | - Silvia Orlandi
- Dipartimento di Chimica Industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, Bologna 40136, Italy
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18
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Martínez-Fernández L, Green JA, Esposito L, Jouybari MY, Zhang Y, Santoro F, Kohler B, Improta R. The photoactivated dynamics of dGpdC and dCpdG sequences in DNA: a comprehensive quantum mechanical study. Chem Sci 2024; 15:9676-9693. [PMID: 38939156 PMCID: PMC11206432 DOI: 10.1039/d4sc00910j] [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: 02/06/2024] [Accepted: 05/04/2024] [Indexed: 06/29/2024] Open
Abstract
Study of alternating DNA GC sequences by different time-resolved spectroscopies has provided fundamental information on the interaction between UV light and DNA, a process of great biological importance. Multiple decay paths have been identified, but their interplay is still poorly understood. Here, we characterize the photophysics of GC-DNA by integrating different computational approaches, to study molecular models including up to 6 bases described at a full quantum mechanical level. Quantum dynamical simulations, exploiting a nonadiabatic linear vibronic coupling (LVC) model, coupled with molecular dynamics sampling of the initial structures of a (GC)5 DNA duplex, provide new insights into the photophysics in the sub-picosecond time-regime. They indicate a substantial population transfer, within 50 fs, from the spectroscopic states towards G → C charge transfer states involving two stacked bases (CTintra), thus explaining the ultrafast disappearance of fluorescence. This picture is consistent with that provided by quantum mechanical geometry optimizations, using time dependent-density functional theory and a polarizable continuum model, which we use to parametrize the LVC model and to map the main excited state deactivation pathways. For the first time, the infrared and excited state absorption signatures of the various states along these pathways are comprehensively mapped. The computational models suggest that the main deactivation pathways, which, according to experiment, lead to ground state recovery on the 10-50 ps time scale, involve CTintra followed by interstrand proton transfer from the neutral G to C-. Our calculations indicate that CTintra is populated to a larger extent and more rapidly in GC than in CG steps and suggest the likely involvement of monomer-like and interstrand charge transfer decay routes for isolated and less stacked CG steps. These findings underscore the importance of the DNA sequence and thermal fluctuations for the dynamics. They will also aid the interpretation of experimental results on other sequences.
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Affiliation(s)
- Lara Martínez-Fernández
- Departamento de Química Física de Materiales, Instituto de Química Física Blas Cabrera, CSIC 28006 Madrid Spain
| | - James Alexander Green
- Institut für Physikalische Theoretische Chemie, Goethe-Universität Frankfurt am Main Frankfurt am Main Germany
| | - Luciana Esposito
- Istituto di Biostrutture e Bioimmagini-CNR (IBB-CNR) Via De Amicis 95 I-80145 Napoli Italy
| | - Martha Yaghoubi Jouybari
- Department of Chemistry and Biomolecular Sciences, University of Ottawa 10 Marie Curie Ottawa Ontario K1N 6N5 Canada
- National Research Council of Canada 100 Sussex Drive Ottawa Ontario K1A 0R6 Canada
- Istituto di Chimica dei Composti Organometallici (ICCOM-CNR) Area della Ricerca del CNR, Via Moruzzi 1 I-56124 Pisa Italy
| | - Yuyuan Zhang
- Department of Chemistry and Biochemistry, The Ohio State University 100 West 18th Avenue Columbus Ohio 43210 USA
| | - Fabrizio Santoro
- Istituto di Chimica dei Composti Organometallici (ICCOM-CNR) Area della Ricerca del CNR, Via Moruzzi 1 I-56124 Pisa Italy
| | - Bern Kohler
- Department of Chemistry and Biochemistry, The Ohio State University 100 West 18th Avenue Columbus Ohio 43210 USA
| | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini-CNR (IBB-CNR) Via De Amicis 95 I-80145 Napoli Italy
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19
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Patel R, Onyema A, Tang PK, Loverde SM. Conformational Dynamics of the Nucleosomal Histone H2B Tails Revealed by Molecular Dynamics Simulations. J Chem Inf Model 2024; 64:4709-4726. [PMID: 38865599 PMCID: PMC11200259 DOI: 10.1021/acs.jcim.4c00059] [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] [Received: 01/11/2024] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 06/14/2024]
Abstract
Epigenetic modifications of histone N-terminal tails play a critical role in regulating the chromatin structure and biological processes such as transcription and DNA repair. One of the key post-translational modifications (PTMs) is the acetylation of lysine residues on histone tails. Epigenetic modifications are ubiquitous in the development of diseases, such as cancer and neurological disorders. Histone H2B tails are critical regulators of nucleosome dynamics, biological processes, and certain diseases. Here, we report all-atomistic molecular dynamics (MD) simulations of the nucleosome to demonstrate that acetylation of the histone tails changes their conformational space and interaction with DNA. We perform simulations of H2B tails, critical regulators of gene regulation, in both the lysine-acetylated (ACK) and unacetylated wild type (WT) states. To explore the effects of salt concentration, we use two different NaCl concentrations to perform simulations at microsecond time scales. Salt can modulate the effects of electrostatic interactions between the DNA phosphate backbone and histone tails. Upon acetylation, H2B tails shift their secondary structure helical propensity. The number of contacts between the DNA and the H2B tail decreases. We characterize the conformational dynamics of the H2B tails by principal component analysis (PCA). The ACK tails become more compact at increased salt concentrations, but conformations from the WT tails display the most contacts with DNA at both salt concentrations. Mainly, H2B acetylation may increase the DNA accessibility for regulatory proteins to bind, which can aid in gene regulation and NCP stability.
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Affiliation(s)
- Rutika Patel
- Ph.D.
Program in Biochemistry, The Graduate Center
of the City University of New York, New York, New York 10016, United States
- Department
of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, New
York, New York 10314, United States
| | - Augustine Onyema
- Ph.D.
Program in Biochemistry, The Graduate Center
of the City University of New York, New York, New York 10016, United States
- Department
of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, New
York, New York 10314, United States
| | - Phu K. Tang
- Ph.D.
Program in Biochemistry, The Graduate Center
of the City University of New York, New York, New York 10016, United States
- Department
of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, New
York, New York 10314, United States
| | - Sharon M. Loverde
- Ph.D.
Program in Biochemistry, The Graduate Center
of the City University of New York, New York, New York 10016, United States
- Department
of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, New
York, New York 10314, United States
- Ph.D.
Program in Chemistry, The Graduate Center
of the City University of New York, New York, New York 10016, United States
- Ph.D.
Program in Physics, The Graduate Center
of the City University of New York, New York, New York 10016, United States
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20
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Tao Y, Giese TJ, Ekesan Ş, Zeng J, Aradi B, Hourahine B, Aktulga HM, Götz AW, Merz KM, York DM. Amber free energy tools: Interoperable software for free energy simulations using generalized quantum mechanical/molecular mechanical and machine learning potentials. J Chem Phys 2024; 160:224104. [PMID: 38856060 DOI: 10.1063/5.0211276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 05/15/2024] [Indexed: 06/11/2024] Open
Abstract
We report the development and testing of new integrated cyberinfrastructure for performing free energy simulations with generalized hybrid quantum mechanical/molecular mechanical (QM/MM) and machine learning potentials (MLPs) in Amber. The Sander molecular dynamics program has been extended to leverage fast, density-functional tight-binding models implemented in the DFTB+ and xTB packages, and an interface to the DeePMD-kit software enables the use of MLPs. The software is integrated through application program interfaces that circumvent the need to perform "system calls" and enable the incorporation of long-range Ewald electrostatics into the external software's self-consistent field procedure. The infrastructure provides access to QM/MM models that may serve as the foundation for QM/MM-ΔMLP potentials, which supplement the semiempirical QM/MM model with a MLP correction trained to reproduce ab initio QM/MM energies and forces. Efficient optimization of minimum free energy pathways is enabled through a new surface-accelerated finite-temperature string method implemented in the FE-ToolKit package. Furthermore, we interfaced Sander with the i-PI software by implementing the socket communication protocol used in the i-PI client-server model. The new interface with i-PI allows for the treatment of nuclear quantum effects with semiempirical QM/MM-ΔMLP models. The modular interoperable software is demonstrated on proton transfer reactions in guanine-thymine mispairs in a B-form deoxyribonucleic acid helix. The current work represents a considerable advance in the development of modular software for performing free energy simulations of chemical reactions that are important in a wide range of applications.
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Affiliation(s)
- Yujun Tao
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Timothy J Giese
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Şölen Ekesan
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Jinzhe Zeng
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Bálint Aradi
- Bremen Center for Computational Materials Science, University of Bremen, D-28334 Bremen, Germany
| | - Ben Hourahine
- SUPA, Department of Physics, University of Strathclyde, Glasgow G4 0NG, United Kingdom
| | - Hasan Metin Aktulga
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
| | - Andreas W Götz
- San Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093, USA
| | - Kenneth M Merz
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
| | - Darrin M York
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
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21
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Tao Y, Giese TJ, York DM. Electronic and Nuclear Quantum Effects on Proton Transfer Reactions of Guanine-Thymine (G-T) Mispairs Using Combined Quantum Mechanical/Molecular Mechanical and Machine Learning Potentials. Molecules 2024; 29:2703. [PMID: 38893576 PMCID: PMC11173453 DOI: 10.3390/molecules29112703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 05/30/2024] [Accepted: 06/04/2024] [Indexed: 06/21/2024] Open
Abstract
Rare tautomeric forms of nucleobases can lead to Watson-Crick-like (WC-like) mispairs in DNA, but the process of proton transfer is fast and difficult to detect experimentally. NMR studies show evidence for the existence of short-time WC-like guanine-thymine (G-T) mispairs; however, the mechanism of proton transfer and the degree to which nuclear quantum effects play a role are unclear. We use a B-DNA helix exhibiting a wGT mispair as a model system to study tautomerization reactions. We perform ab initio (PBE0/6-31G*) quantum mechanical/molecular mechanical (QM/MM) simulations to examine the free energy surface for tautomerization. We demonstrate that while the ab initio QM/MM simulations are accurate, considerable sampling is required to achieve high precision in the free energy barriers. To address this problem, we develop a QM/MM machine learning potential correction (QM/MM-ΔMLP) that is able to improve the computational efficiency, greatly extend the accessible time scales of the simulations, and enable practical application of path integral molecular dynamics to examine nuclear quantum effects. We find that the inclusion of nuclear quantum effects has only a modest effect on the mechanistic pathway but leads to a considerable lowering of the free energy barrier for the GT*⇌G*T equilibrium. Our results enable a rationalization of observed experimental data and the prediction of populations of rare tautomeric forms of nucleobases and rates of their interconversion in B-DNA.
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22
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Hu Y, Liu J, Ke Y, Wang B, Lim JYC, Dong Z, Long Y, Willner I. Oligo-Adenine and Cyanuric Acid Supramolecular DNA-Based Hydrogels Exhibiting Acid-Resistance and Physiological pH-Responsiveness. ACS APPLIED MATERIALS & INTERFACES 2024; 16:29235-29247. [PMID: 38769743 DOI: 10.1021/acsami.4c03834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Expanding the functions and applications of DNA by integrating noncanonical bases and structures into biopolymers is a continuous scientific effort. An adenine-rich strand (A-strand) is introduced as functional scaffold revealing, in the presence of the low-molecular-weight cofactor cyanuric acid (CA, pKa 6.9), supramolecular hydrogel-forming efficacies demonstrating multiple pH-responsiveness. At pH 1.2, the A-strand transforms into a parallel A-motif duplex hydrogel cross-linked by AH+-H+A units due to the protonation of adenine (pKa 3.5). At pH 5.2, and in the presence of coadded CA, a helicene-like configuration is formed between adenine and protonated CA, generating a parallel A-CA triplex cross-linked hydrogel. At pH 8.0, the hydrogel undergoes transition into a liquid state by deprotonation of CA cofactor units and disassembly of A-CA triplex into its constituent components. Density functional theory calculations and molecular dynamics simulations, supporting the structural reconfigurations of A-strand in the presence of CA, are performed. The sequential pH-stimulated hydrogel states are rheometrically characterized. The hydrogel framework is loaded with fluorescein-labeled insulin, and the pH-stimulated release of insulin from the hydrogel across the pH barriers present in the gastrointestinal tract is demonstrated. The results provide principles for future application of the hydrogel for oral insulin administration for diabetes.
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Affiliation(s)
- Yuwei Hu
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, Singapore 138634, Republic of Singapore
| | - Jia Liu
- State Key Laboratory Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Yujie Ke
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, Singapore 138634, Republic of Singapore
| | - Binju Wang
- State Key Laboratory Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Jason Y C Lim
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, Singapore 138634, Republic of Singapore
| | - Zhaogang Dong
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, Singapore 138634, Republic of Singapore
| | - Yi Long
- Electronic Engineering Department, The Chinese University of Hong Kong, Hong Kong 999077, P. R. China
| | - Itamar Willner
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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23
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Sun T, Korolev N, Minhas V, Mirzoev A, Lyubartsev AP, Nordenskiöld L. Multiscale modeling reveals the ion-mediated phase separation of nucleosome core particles. Biophys J 2024; 123:1414-1434. [PMID: 37915169 PMCID: PMC11163297 DOI: 10.1016/j.bpj.2023.10.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/05/2023] [Accepted: 10/27/2023] [Indexed: 11/03/2023] Open
Abstract
Due to the vast length scale inside the cell nucleus, multiscale models are required to understand chromatin folding, structure, and dynamics and how they regulate genomic activities such as DNA transcription, replication, and repair. We study the interactions and structure of condensed phases formed by the universal building block of chromatin, the nucleosome core particle (NCP), using bottom-up multiscale coarse-grained (CG) simulations with a model extracted from all-atom MD simulations. In the presence of the multivalent cations Mg(H2O)62+ or CoHex3+, we analyze the internal structures of the NCP aggregates and the contributions of histone tails and ions to the aggregation patterns. We then derive a "super" coarse-grained (SCG) NCP model to study the macroscopic scale phase separation of NCPs. The SCG simulations show the formation of NCP aggregates with Mg(H2O)62+ concentration-dependent densities and sizes. Variation of the CoHex3+ concentrations results in highly ordered lamellocolumnar and hexagonal columnar phases in agreement with experimental data. The results give detailed insights into nucleosome interactions and for understanding chromatin folding in the cell nucleus.
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Affiliation(s)
- Tiedong Sun
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Nikolay Korolev
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Vishal Minhas
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Alexander Mirzoev
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Alexander P Lyubartsev
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden.
| | - Lars Nordenskiöld
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
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24
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Park J, Herrmann GK, Roy A, Shumate CK, Cisneros GA, Yin YW. An interaction network in the polymerase active site is a prerequisite for Watson-Crick base pairing in Pol γ. SCIENCE ADVANCES 2024; 10:eadl3214. [PMID: 38787958 PMCID: PMC11122685 DOI: 10.1126/sciadv.adl3214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 04/18/2024] [Indexed: 05/26/2024]
Abstract
The replication accuracy of DNA polymerase gamma (Pol γ) is essential for mitochondrial genome integrity. Mutation of human Pol γ arginine-853 has been linked to neurological diseases. Although not a catalytic residue, Pol γ arginine-853 mutants are void of polymerase activity. To identify the structural basis for the disease, we determined a crystal structure of the Pol γ mutant ternary complex with correct incoming nucleotide 2'-deoxycytidine 5'-triphosphate (dCTP). Opposite to the wild type that undergoes open-to-closed conformational changes when bound to a correct nucleotide that is essential for forming a catalytically competent active site, the mutant complex failed to undergo the conformational change, and the dCTP did not base pair with its Watson-Crick complementary templating residue. Our studies revealed that arginine-853 coordinates an interaction network that aligns the 3'-end of primer and dCTP with the catalytic residues. Disruption of the network precludes the formation of Watson-Crick base pairing and closing of the active site, resulting in an inactive polymerase.
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Affiliation(s)
- Joon Park
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Geoffrey K. Herrmann
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Arkanil Roy
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, TX 75080, USA
| | - Christie K. Shumate
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - G. Andrés Cisneros
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, TX 75080, USA
- Department of Physics, University of Texas at Dallas, Richardson, TX 75080, USA
| | - Y. Whitney Yin
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA
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25
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Wang X, Huang T, Li L, Xu Y. Effect of temperature on anisotropic bending elasticity of dsRNA: an all-atom molecular dynamics simulation. RSC Adv 2024; 14:17170-17177. [PMID: 38808231 PMCID: PMC11130765 DOI: 10.1039/d4ra02354d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 05/17/2024] [Indexed: 05/30/2024] Open
Abstract
Employing all-atom molecular dynamics simulations, we examined the temperature-dependent behavior of bending elasticity in double-stranded RNA (dsRNA). Specifically, we focused on the bending persistence length and its constituent components, namely, the tilt and roll stiffness. Our results revealed a near-linear decrease in these stiffness components as a function of temperature, thereby highlighting the increased flexibility of dsRNA at elevated temperatures. Furthermore, our data revealed a significant anisotropy in dsRNA bending elasticity, which diminished with increasing temperature, attributable to marked disparities in tilt and roll stiffness components. We delineated the underlying biophysical mechanisms and corroborated our findings with extant literature. These observations offer salient implications for advancing our understanding of nucleic acid elasticity, and are pertinent to potential medical applications.
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Affiliation(s)
- Xianghong Wang
- School of Sino-German Engineering, Shanghai Technical Institute of Electronics and Information Shanghai 201411 China
| | - Tingting Huang
- School of Sino-German Engineering, Shanghai Technical Institute of Electronics and Information Shanghai 201411 China
| | - Liyun Li
- Department of Physics, Wenzhou University Wenzhou 325035 China
| | - Yanliang Xu
- School of Sino-German Engineering, Shanghai Technical Institute of Electronics and Information Shanghai 201411 China
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26
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Xu J, Hao J, Bu C, Meng Y, Xiao H, Zhang M, Li C. XMECP: Reaching State-of-the-Art MECP Optimization in Multiscale Complex Systems. J Chem Theory Comput 2024; 20:3590-3600. [PMID: 38651739 DOI: 10.1021/acs.jctc.4c00033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
The Python-based program, XMECP, is developed for realizing robust, efficient, and state-of-the-art minimum energy crossing point (MECP) optimization in multiscale complex systems. This article introduces the basic capabilities of the XMECP program by theoretically investigating the MECP mechanism of several example systems including (1) the photosensitization mechanism of benzophenone, (2) photoinduced proton-coupled electron transfer in the cytosine-guanine base pair in DNA, (3) the spin-flip process in oxygen activation catalyzed by an iron-containing 2-oxoglutarate-dependent oxygenase (Fe/2OGX), and (4) the photochemical pathway of flavoprotein adjusted by the intensity of an external electric field. MECPs related to multistate reaction and multistate reactivity in large-scale complex biochemical systems can be well-treated by workflows suggested by the XMECP program. The branching plane updating the MECP optimization algorithm is strongly recommended as it provides derivative coupling vector (DCV) with explicit calculation and can equivalently evaluate contributions from non-QM residues to DCV, which can be nonadiabatic coupling or spin-orbit coupling in different cases. In the discussed QM/MM examples, we also found that the influence on the QM region by DCV can occur through noncovalent interactions and decay with distance. In the example of DNA base pairs, the nonadiabatic coupling occurs across the π-π stacking structure formed in the double-helix system. In contrast to general intuition, in the example of Fe/2OGX, the central ferrous and oxygen part contribute little to the spin-orbit coupling; however, a nearby arginine residue, which is treated by molecular mechanics in the QM/MM method, contributes significantly via two hydrogen bonds formed with α-ketoglutarate (α-KG). This indicates that the arginine residue plays a significant role in oxygen activation, driving the initial triplet state toward the productive quintet state, which is more than the previous knowledge that the arginine residue can bind α-KG at the reaction site by hydrogen bonds.
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Affiliation(s)
- Jiawei Xu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, Fujian, P. R. China
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Jian Hao
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, Fujian, P. R. China
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Caijie Bu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, Fujian, P. R. China
- College of Chemistry and Materials Science, Fujian Normal University, Fuzhou 350117, Fujian, P. R. China
| | - Yajie Meng
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, Fujian, P. R. China
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Han Xiao
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, Fujian, P. R. China
| | - Minyi Zhang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, Fujian, P. R. China
| | - Chunsen Li
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, Fujian, P. R. China
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen University, Xiamen 361005, Fujian, P. R. China
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27
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Xie T, He Z, Zhang D, Zhou R. Directional Pumpless Transport of Biomolecules through Self-Propelled Nanodroplets on Patterned Heterostructures. J Phys Chem B 2024. [PMID: 38709975 DOI: 10.1021/acs.jpcb.3c06786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
The surface patterning in natural systems has exhibited appreciable functional advantages for life activities, which serve as inspiration for the design of artificial counterparts to achieve functions such as directional liquid transport at the nanoscale. Here, we propose a patterned two-dimensional (2D) in-plane heterostructure with a triangle-shaped hexagonal boron nitride (hBN) track embedded in graphene nanosheets, which can achieve unidirectional and self-propelled transport of nanodroplets carrying various biomolecules such as DNA, RNA, and peptides. Our extensive MD simulations show that the wettability gradient on the patterned heterostructure can drive the motion of nanodroplet with an instantaneous acceleration, which also permits long-distance transport (>100 nm) at the microsecond time scale. The different behaviors of various types of biomolecules have been further studied systematically within the transporting nanodroplets. These findings suggest that these specially designed, patterned heterostructures have the potential for spontaneous, directional transport of important biomolecules, which might be useful in biosensing, drug delivery, and biomedical nanodevices.
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Affiliation(s)
- Teng Xie
- College of Life Sciences and Institute of Quantitative Biology, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Zhi He
- College of Life Sciences and Institute of Quantitative Biology, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Dong Zhang
- College of Life Sciences and Institute of Quantitative Biology, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Ruhong Zhou
- College of Life Sciences and Institute of Quantitative Biology, Zhejiang University, Hangzhou, Zhejiang 310058, China
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28
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Orndorff PB, van der Vaart A. Systematic assessment of the flexibility of uracil damaged DNA. J Biomol Struct Dyn 2024; 42:3958-3968. [PMID: 37261803 DOI: 10.1080/07391102.2023.2217683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 05/17/2023] [Indexed: 06/02/2023]
Abstract
Uracil is a common DNA lesion which is recognized and removed by uracil DNA-glycosylase (UDG) as a part of the base excision repair pathway. Excision proceeds by base flipping, and UDG efficiency is thought to depend on the ease of deformability of the bases neighboring the lesion. We used molecular dynamics simulations to assess the flexibility of a large library of dsDNA strands, containing all tetranucleotide motifs with U:A, U:G, T:A or C:G base pairs. Our study demonstrates that uracil damaged DNA largely follows trends in flexibility of undamaged DNA. Measured bending persistence lengths, groove widths, step parameters and base flipping propensities demonstrate that uracil increases the flexibility of DNA, and that U:G base paired strands are more flexible than U:A strands. Certain sequence contexts are more deformable than others, with a key role for the 3' base next to uracil. Flexibilities are large when this base is an A or G, and repressed for a C or T. A 5' T adjacent to the uracil strongly promotes flexibility, but other 5' bases are less influential. DNA bending is correlated to step deformations and base flipping, and bending aids flipping. Our study implies that the link between substrate flexibility and UDG efficiency is widely valid, helps explain why UDG prefers to bind U:G base paired strands, and suggests that the DNA bending angle of the UDG-substrate complex is optimal for base flipping.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Paul B Orndorff
- Department of Chemistry, University of South Florida, Tampa, Florida, USA
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29
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Umezawa K, Ikeda R, Sakamoto T, Enomoto Y, Nihashi Y, Shinji S, Shimosato T, Kagami H, Takaya T. Development of the 12-Base Short Dimeric Myogenetic Oligodeoxynucleotide That Induces Myogenic Differentiation. BIOTECH 2024; 13:11. [PMID: 38804293 PMCID: PMC11130974 DOI: 10.3390/biotech13020011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/29/2024] Open
Abstract
A myogenetic oligodeoxynucleotide (myoDN), iSN04 (5'-AGA TTA GGG TGA GGG TGA-3'), is a single-stranded 18-base telomeric DNA that serves as an anti-nucleolin aptamer and induces myogenic differentiation, which is expected to be a nucleic acid drug for the prevention of disease-associated muscle wasting. To improve the drug efficacy and synthesis cost of myoDN, shortening the sequence while maintaining its structure-based function is a major challenge. Here, we report the novel 12-base non-telomeric myoDN, iMyo01 (5'-TTG GGT GGG GAA-3'), which has comparable myogenic activity to iSN04. iMyo01 as well as iSN04 promoted myotube formation of primary-cultured human myoblasts with upregulation of myogenic gene expression. Both iMyo01 and iSN04 interacted with nucleolin, but iMyo01 did not bind to berberine, the isoquinoline alkaloid that stabilizes iSN04. Nuclear magnetic resonance revealed that iMyo01 forms a G-quadruplex structure despite its short sequence. Native polyacrylamide gel electrophoresis and a computational molecular dynamics simulation indicated that iMyo01 forms a homodimer to generate a G-quadruplex. These results provide new insights into the aptamer truncation technology that preserves aptamer conformation and bioactivity for the development of efficient nucleic acid drugs.
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Affiliation(s)
- Koji Umezawa
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, 8304 Minami-minowa, Kami-ina 399-4598, Japan; (K.U.); (Y.E.); (T.S.); (H.K.)
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, 8304 Minami-minowa, Kami-ina 399-4598, Japan
| | - Rena Ikeda
- Department of Agriculture, Graduate School of Science and Technology, Shinshu University, 8304 Minami-minowa, Kami-ina 399-4598, Japan
| | - Taiichi Sakamoto
- Department of Life Science, Faculty of Advanced Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino-shi 275-0016, Japan;
| | - Yuya Enomoto
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, 8304 Minami-minowa, Kami-ina 399-4598, Japan; (K.U.); (Y.E.); (T.S.); (H.K.)
| | - Yuma Nihashi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Centoral 5-41, 1-1-1 Higashi, Tsukuba 305-8565, Japan;
| | - Sayaka Shinji
- Department of Agriculture, Graduate School of Science and Technology, Shinshu University, 8304 Minami-minowa, Kami-ina 399-4598, Japan
| | - Takeshi Shimosato
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, 8304 Minami-minowa, Kami-ina 399-4598, Japan; (K.U.); (Y.E.); (T.S.); (H.K.)
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, 8304 Minami-minowa, Kami-ina 399-4598, Japan
- Department of Agriculture, Graduate School of Science and Technology, Shinshu University, 8304 Minami-minowa, Kami-ina 399-4598, Japan
| | - Hiroshi Kagami
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, 8304 Minami-minowa, Kami-ina 399-4598, Japan; (K.U.); (Y.E.); (T.S.); (H.K.)
| | - Tomohide Takaya
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, 8304 Minami-minowa, Kami-ina 399-4598, Japan; (K.U.); (Y.E.); (T.S.); (H.K.)
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, 8304 Minami-minowa, Kami-ina 399-4598, Japan
- Department of Agriculture, Graduate School of Science and Technology, Shinshu University, 8304 Minami-minowa, Kami-ina 399-4598, Japan
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30
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Peng J, Liang G, Li Y, Mao S, Zhang C, Wang Y, Li Z. Identification of a novel FOXO3 agonist that protects against alcohol induced liver injury. Biochem Biophys Res Commun 2024; 704:149690. [PMID: 38387326 DOI: 10.1016/j.bbrc.2024.149690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 02/07/2024] [Accepted: 02/13/2024] [Indexed: 02/24/2024]
Abstract
Alcohol-related liver disease (ALD) is a global healthcare concern which caused by excessive alcohol consumption with limited treatment options. The pathogenesis of ALD is complex and involves in hepatocyte damage, hepatic inflammation, increased gut permeability and microbiome dysbiosis. FOXO3 is a well-recognized transcription factor which associated with longevity via promoting antioxidant stress response, preventing senescence and cell death, and inhibiting inflammation. We and many others have reported that FOXO3-/- mice develop more severe liver injury in response to alcohol. In the present study, we aimed to develop compounds that activate FOXO3 and further investigate their effects in alcohol induced liver injury. Through virtual screening, we discovered series of small molecular compounds that showed high affinity to FOXO3. We confirmed effects of compounds on FOXO3 target gene expression, as well as antioxidant and anti-apoptotic effects in vitro. Subsequently we evaluated the protective efficacy of compounds in alcohol induced liver injury in vivo. As a result, the leading compound we identified, 214991, activated downstream target genes expression of FOXO3, inhibited intracellular ROS accumulation and cell apoptosis induced by H2O2 and sorafenib. By using Lieber-DeCarli alcohol feeding mouse model, 214991 showed protective effects against alcohol-induced liver inflammation, macrophage and neutrophil infiltration, and steatosis. These findings not only reinforce the potential of FOXO3 as a valuable target for therapeutic intervention of ALD, but also suggested that compound 214991 as a promising candidate for the development of innovative therapeutic strategies of ALD.
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Affiliation(s)
- Jinying Peng
- The Key Laboratory of Study and Discovery of Small Targeted Molecules of Hunan Province, The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province and Department of Pharmacy, School of Medicine, Hunan Normal University, Hunan, 410013, China
| | - Gaoshuang Liang
- The Key Laboratory of Study and Discovery of Small Targeted Molecules of Hunan Province, The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province and Department of Pharmacy, School of Medicine, Hunan Normal University, Hunan, 410013, China
| | - Yaqi Li
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Hunan, 410081, China; Institute of Interdisciplinary Studies, Hunan Normal University, Hunan, 410081, China; Peptide and Small Molecule Drug R&D Plateform, Furong Laboratory, Hunan Normal University, Hunan, 410081, China
| | - Siyu Mao
- The Key Laboratory of Study and Discovery of Small Targeted Molecules of Hunan Province, The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province and Department of Pharmacy, School of Medicine, Hunan Normal University, Hunan, 410013, China
| | - Chen Zhang
- The Key Laboratory of Study and Discovery of Small Targeted Molecules of Hunan Province, The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province and Department of Pharmacy, School of Medicine, Hunan Normal University, Hunan, 410013, China
| | - Ying Wang
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Hunan, 410081, China; Institute of Interdisciplinary Studies, Hunan Normal University, Hunan, 410081, China; Peptide and Small Molecule Drug R&D Plateform, Furong Laboratory, Hunan Normal University, Hunan, 410081, China.
| | - Zhuan Li
- The Key Laboratory of Study and Discovery of Small Targeted Molecules of Hunan Province, The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province and Department of Pharmacy, School of Medicine, Hunan Normal University, Hunan, 410013, China.
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31
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Go YJ, Kalathingal M, Rhee YM. An Ensemble Docking Approach for Analyzing and Designing Aptamer Heterodimers Targeting VEGF 165. Int J Mol Sci 2024; 25:4066. [PMID: 38612876 PMCID: PMC11012306 DOI: 10.3390/ijms25074066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 03/27/2024] [Accepted: 04/02/2024] [Indexed: 04/14/2024] Open
Abstract
Vascular endothelial growth factor 165 (VEGF165) is a prominent isoform of the VEGF-A protein that plays a crucial role in various angiogenesis-related diseases. It is homodimeric, and each of its monomers is composed of two domains connected by a flexible linker. DNA aptamers, which have emerged as potent therapeutic molecules for many proteins with high specificity and affinity, can also work for VEGF165. A DNA aptamer heterodimer composed of monomers of V7t1 and del5-1 connected by a flexible linker (V7t1:del5-1) exhibits a greater binding affinity with VEGF165 compared to either of the two monomers alone. Although the structure of the complex formed between the aptamer heterodimer and VEGF165 is unknown due to the highly flexible linkers, gaining structural information will still be valuable for future developments. Toward this end of accessing structural information, we adopt an ensemble docking approach here. We first obtain an ensemble of structures for both VEGF165 and the aptamer heterodimer by considering both small- and large-scale motions. We then proceed through an extraction process based on ensemble docking, molecular dynamics simulations, and binding free energy calculations to predict the structures of the VEGF165/V7t1:del5-1 complex. Through the same procedures, we reach a new aptamer heterodimer that bears a locked nucleic acid-modified counterpart of V7t1, namely RNV66:del5-1, which also binds well with VEGF165. We apply the same protocol to the monomeric units V7t1, RNV66, and del5-1 to target VEGF165. We observe that V7t1:del5-1 and RNV66:del5-1 show higher binding affinities with VEGF165 than any of the monomers, consistent with experiments that support the notion that aptamer heterodimers are more effective anti-VEGF165 aptamers than monomeric aptamers. Among the five different aptamers studied here, the newly designed RNV66:del5-1 shows the highest binding affinity with VEGF165. We expect that our ensemble docking approach can help in de novo designs of homo/heterodimeric anti-angiogenic drugs to target the homodimeric VEGF165.
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Affiliation(s)
- Yeon Ju Go
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea;
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Mahroof Kalathingal
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea;
| | - Young Min Rhee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea;
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32
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Nandi S, Bhaduri S, Das D, Ghosh P, Mandal M, Mitra P. Deciphering the Lexicon of Protein Targets: A Review on Multifaceted Drug Discovery in the Era of Artificial Intelligence. Mol Pharm 2024; 21:1563-1590. [PMID: 38466810 DOI: 10.1021/acs.molpharmaceut.3c01161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Understanding protein sequence and structure is essential for understanding protein-protein interactions (PPIs), which are essential for many biological processes and diseases. Targeting protein binding hot spots, which regulate signaling and growth, with rational drug design is promising. Rational drug design uses structural data and computational tools to study protein binding sites and protein interfaces to design inhibitors that can change these interactions, thereby potentially leading to therapeutic approaches. Artificial intelligence (AI), such as machine learning (ML) and deep learning (DL), has advanced drug discovery and design by providing computational resources and methods. Quantum chemistry is essential for drug reactivity, toxicology, drug screening, and quantitative structure-activity relationship (QSAR) properties. This review discusses the methodologies and challenges of identifying and characterizing hot spots and binding sites. It also explores the strategies and applications of artificial-intelligence-based rational drug design technologies that target proteins and protein-protein interaction (PPI) binding hot spots. It provides valuable insights for drug design with therapeutic implications. We have also demonstrated the pathological conditions of heat shock protein 27 (HSP27) and matrix metallopoproteinases (MMP2 and MMP9) and designed inhibitors of these proteins using the drug discovery paradigm in a case study on the discovery of drug molecules for cancer treatment. Additionally, the implications of benzothiazole derivatives for anticancer drug design and discovery are deliberated.
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Affiliation(s)
- Suvendu Nandi
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
| | - Soumyadeep Bhaduri
- Centre for Computational and Data Sciences, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
| | - Debraj Das
- Centre for Computational and Data Sciences, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
| | - Priya Ghosh
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
| | - Mahitosh Mandal
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
| | - Pralay Mitra
- Department of Computer Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
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33
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Jurkowski M, Kogut M, Sappati S, Czub J. Why Are Left-Handed G-Quadruplexes Scarce? J Phys Chem Lett 2024; 15:3142-3148. [PMID: 38477716 PMCID: PMC10961827 DOI: 10.1021/acs.jpclett.3c03589] [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] [Received: 12/23/2023] [Revised: 02/27/2024] [Accepted: 03/08/2024] [Indexed: 03/14/2024]
Abstract
G-quadruplexes (G4s) are nucleic acid structures crucial for the regulation of gene expression and genome maintenance. While they hold promise as nanodevice components, achieving desired G4 folds requires understanding the interplay between stability and structural properties, like helicity. Although right-handed G4 structures dominate the experimental data, the molecular basis for this preference over left-handed helicity is unclear. To address this, we employ all-atom molecular dynamics simulations and quantum chemical methods. Our results reveal that right-handed G4s exhibit greater thermodynamic and kinetic stability as a result of favorable sugar-phosphate backbone conformations in guanine tracts. Moreover, while hydrogen-bonding patterns influence helicity-specific G4 loop conformations, they minimally affect stability differences. We also elucidate the strong correlation between helicity and the strand progression direction, essential for G4 structures. These findings deepen our understanding of G4s, providing molecular-level insights into their structural and energetic preferences, which could inform the design of novel nanodevices.
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Affiliation(s)
- Michał Jurkowski
- Department
of Physical Chemistry, Gdańsk University
of Technology, Narutowicza Street 11/12, 80-233 Gdańsk, Poland
| | - Mateusz Kogut
- Department
of Physical Chemistry, Gdańsk University
of Technology, Narutowicza Street 11/12, 80-233 Gdańsk, Poland
| | - Subrahmanyam Sappati
- Department
of Physical Chemistry, Gdańsk University
of Technology, Narutowicza Street 11/12, 80-233 Gdańsk, Poland
- BioTechMed
Center, Gdańsk University of Technology, Narutowicza Street 11/12, 80-233 Gdańsk, Poland
| | - Jacek Czub
- Department
of Physical Chemistry, Gdańsk University
of Technology, Narutowicza Street 11/12, 80-233 Gdańsk, Poland
- BioTechMed
Center, Gdańsk University of Technology, Narutowicza Street 11/12, 80-233 Gdańsk, Poland
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34
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Kaur R, Frederickson A, Wetmore SD. Elucidation of the catalytic mechanism of a single-metal dependent homing endonuclease using QM and QM/MM approaches: the case study of I- PpoI. Phys Chem Chem Phys 2024; 26:8919-8931. [PMID: 38426850 DOI: 10.1039/d3cp06201e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Homing endonucleases (HEs) are highly specific DNA cleaving enzymes, with I-PpoI having been suggested to use a single metal to accelerate phosphodiester bond cleavage. Although an I-PpoI mechanism has been proposed based on experimental structural data, no consensus has been reached regarding the roles of the metal or key active site amino acids. This study uses QM cluster and QM/MM calculations to provide atomic-level details of the I-PpoI catalytic mechanism. Minimal QM cluster and large-scale QM/MM models demonstrate that the experimentally-proposed pathway involving direct Mg2+ coordination to the substrate coupled with leaving group protonation through a metal-activated water is not feasible due to an inconducive I-PpoI active site alignment. Despite QM cluster models of varying size uncovering a pathway involving leaving group protonation by a metal-activated water, indirect (water-mediated) metal coordination to the substrate is required to afford this pathway, which renders this mechanism energetically infeasible. Instead, QM cluster models reveal that the preferred pathway involves direct Mg2+-O3' coordination to stabilize the charged substrate and assist leaving group departure, while H98 activates the water nucleophile. These calculations also underscore that both catalytic residues that directly interact with the substrate and secondary amino acids that position or stabilize these residues are required for efficient catalysis. QM/MM calculations on the solvated enzyme-DNA complex verify the preferred mechanism, which is fully consistent with experimental kinetic, structural, and mutational data. The fundamental understanding of the I-PpoI mechanism of action, gained from the present work can be used to further explore potential uses of this enzyme in biotechnology and medicine, and direct future computational investigations of other members of the understudied HE family.
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Affiliation(s)
- Rajwinder Kaur
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada.
| | - Angela Frederickson
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada.
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada.
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35
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Roldán-Piñero C, Luengo-Márquez J, Assenza S, Pérez R. Systematic Comparison of Atomistic Force Fields for the Mechanical Properties of Double-Stranded DNA. J Chem Theory Comput 2024; 20:2261-2272. [PMID: 38411091 PMCID: PMC10938644 DOI: 10.1021/acs.jctc.3c01089] [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] [Received: 10/02/2023] [Revised: 02/14/2024] [Accepted: 02/14/2024] [Indexed: 02/28/2024]
Abstract
The response of double-stranded DNA to external mechanical stress plays a central role in its interactions with the protein machinery in the cell. Modern atomistic force fields have been shown to provide highly accurate predictions for the fine structural features of the duplex. In contrast, and despite their pivotal function, less attention has been devoted to the accuracy of the prediction of the elastic parameters. Several reports have addressed the flexibility of double-stranded DNA via all-atom molecular dynamics, yet the collected information is insufficient to have a clear understanding of the relative performance of the various force fields. In this work, we fill this gap by performing a systematic study in which several systems, characterized by different sequence contexts, are simulated with the most popular force fields within the AMBER family, bcs1 and OL15, as well as with CHARMM36. Analysis of our results, together with their comparison with previous work focused on bsc0, allows us to unveil the differences in the predicted rigidity between the newest force fields and suggests a roadmap to test their performance against experiments. In the case of the stretch modulus, we reconcile these differences, showing that a single mapping between sequence-dependent conformation and elasticity via the crookedness parameter captures simultaneously the results of all force fields, supporting the key role of crookedness in the mechanical response of double-stranded DNA.
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Affiliation(s)
- Carlos Roldán-Piñero
- Departamento
de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
| | - Juan Luengo-Márquez
- Departamento
de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
- Instituto
Nicolás Cabrera, Universidad Autónoma
de Madrid, E-28049 Madrid, Spain
| | - Salvatore Assenza
- Departamento
de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
- Instituto
Nicolás Cabrera, Universidad Autónoma
de Madrid, E-28049 Madrid, Spain
- Condensed
Matter Physics Center (IFIMAC), Universidad
Autónoma de Madrid, E-28049 Madrid, Spain
| | - Rubén Pérez
- Departamento
de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
- Condensed
Matter Physics Center (IFIMAC), Universidad
Autónoma de Madrid, E-28049 Madrid, Spain
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36
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Mondal S, Mukherjee S, Bagchi B. Melting and Bubble Formation in a Double-Stranded DNA: Microscopic Aspects of Early Base-Pair Opening Events and the Role of Water. J Phys Chem B 2024; 128:2076-2086. [PMID: 38389118 DOI: 10.1021/acs.jpcb.3c06519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Despite its rigid structure, DNA is a remarkably flexible molecule. Flexibility is essential for biological functions (such as transcription and gene repair), which require large-amplitude structural changes such as bubble formation. The bubbles thus formed are required to have a certain stability of their own and survive long on the time scale of molecular motions. A molecular understanding of fluctuations leading to quasi-stable structures is not available. Through extensive atomistic molecular dynamics simulations, we identify a sequence of microscopic events that culminate in local bubble formation, which is initiated by base-pair (BP) opening, resulting from the cleavage of native BP hydrogen bonds (HBs). This is followed by the formation of mismatched BPs with non-native contacts. These metastable structures can either revert to their original forms or undergo a flipping transition to form a local bubble that can span across 3-4 BPs. A substantial distortion of the DNA backbone and a disruption of BP stacking are observed because of the structural changes induced by these local perturbations. We also explored how water helps in the entire process. A small number of water molecules undergo rearrangement to stabilize the intermediate states by forming HBs with DNA bases. Water thus acts as a lubricant that counteracts the enthalpic penalty suffered from the loss of native BP contacts. Although the process of bubble formation is reversible, the sequence of steps involved poses an entropic barrier, preventing it from easily retracing the path to the native state.
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Affiliation(s)
- Sayantan Mondal
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Saumyak Mukherjee
- Center for Theoretical Chemistry, Ruhr University Bochum, Universitätsstraße 150, Bochum D-44780, Germany
| | - Biman Bagchi
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
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37
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Zhang Z, Mou X, Zhang Y, He L, Li S. Influence of temperature on bend, twist and twist-bend coupling of dsDNA. Phys Chem Chem Phys 2024; 26:8077-8088. [PMID: 38224130 DOI: 10.1039/d3cp04932a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
The temperature-dependent bend and twist elasticities of dsDNA, as well as their couplings, were explored through all-atom molecular dynamics simulations. Three rotational parameters, tilt, roll, and twist, were employed to assess the bend and twist elasticities through their stiffness matrix. Our analysis indicates that the bend and twist stiffnesses decrease as the temperature rises, primarily owing to entropic influences stemming from thermodynamic fluctuations. Furthermore, the couplings between these rotational parameters also exhibit a decline with increasing temperature, although the roll-twist coupling displays greater strength than the tilt-roll and tilt-twist couplings, attributed to its more robust correction component. We elucidated the influence of temperature on bend and twist elasticities based on the comparisons between various models and existing data.
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Affiliation(s)
- Zihao Zhang
- Department of Physics, Wenzhou University, Wenzhou, 325035, China.
| | - Xuankang Mou
- Department of Physics, Wenzhou University, Wenzhou, 325035, China.
| | - Yahong Zhang
- Department of Physics, Wenzhou University, Wenzhou, 325035, China.
| | - Linli He
- Department of Physics, Wenzhou University, Wenzhou, 325035, China.
| | - Shiben Li
- Department of Physics, Wenzhou University, Wenzhou, 325035, China.
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38
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Dohnalová H, Matoušková E, Lankaš F. Temperature-dependent elasticity of DNA, RNA, and hybrid double helices. Biophys J 2024; 123:572-583. [PMID: 38340722 PMCID: PMC10938081 DOI: 10.1016/j.bpj.2024.01.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 12/19/2023] [Accepted: 01/26/2024] [Indexed: 02/12/2024] Open
Abstract
Nucleic acid double helices in their DNA, RNA, and DNA-RNA hybrid form play a fundamental role in biology and are main building blocks of artificial nanostructures, but how their properties depend on temperature remains poorly understood. Here, we report thermal dependence of dynamic bending persistence length, twist rigidity, stretch modulus, and twist-stretch coupling for DNA, RNA, and hybrid duplexes between 7°C and 47°C. The results are based on all-atom molecular dynamics simulations using different force field parameterizations. We first demonstrate that unrestrained molecular dynamics can reproduce experimentally known mechanical properties of the duplexes at room temperature. Beyond experimentally known features, we also infer the twist rigidity and twist-stretch coupling of the hybrid duplex. As for the temperature dependence, we found that increasing temperature softens all the duplexes with respect to bending, twisting, and stretching. The relative decrease of the stretch moduli is 0.003-0.004/°C, similar for all the duplex variants despite their very different stretching stiffness, whereas RNA twist stiffness decreases by 0.003/°C, and smaller values are found for the other elastic moduli. The twist-stretch couplings are nearly unaffected by temperature. The stretching, bending, and twisting stiffness all include an important entropic component. Relation of our results to the two-state model of DNA flexibility is discussed. Our work provides temperature-dependent elasticity of nucleic acid duplexes at the microsecond scale relevant for initial stages of protein binding.
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Affiliation(s)
- Hana Dohnalová
- Department of Informatics and Chemistry, University of Chemistry and Technology Prague, Praha 6, Czech Republic
| | - Eva Matoušková
- Department of Informatics and Chemistry, University of Chemistry and Technology Prague, Praha 6, Czech Republic
| | - Filip Lankaš
- Department of Informatics and Chemistry, University of Chemistry and Technology Prague, Praha 6, Czech Republic.
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39
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Liu B, Qi Y, Wang X, Gao X, Yao Y, Zhang L. Investigation of the Flipping Dynamics of 1, N6-Ethenoadenine in Alkyladenine DNA Glycosylase. J Phys Chem B 2024; 128:1606-1617. [PMID: 38331753 DOI: 10.1021/acs.jpcb.3c06853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
Alkyladenine DNA glycosylase (AAG) is an essential enzyme responsible for maintaining genome integrity by repairing several DNA lesions damaged by alkylation or deamination. Understanding how it can recognize and excise the lesions thus lays the foundation for therapeutic treatment against lesion-associated diseases or cancers. However, the molecular details of how the lesion can be distinguished from the matched base by AAG and how it enters the cleavage site, ready for excision, are not fully elucidated. In this study, we have revealed the molecular details of the flipping dynamics of 1, N6-ethenoadenine (εA) not only in the form of free double-stranded DNA (dsDNA) but also in the form of the AAG-dsDNA complex. Our MD simulations and PMF calculations have shown that the flipping of εA and dA is thermodynamically disfavored in the free dsDNA, even though εA has a lower flipping energy barrier than dA. By sharp contrast, the flipping of εA is thermodynamically favored in AAG with an obvious free energy drop, while dA is equally stabilized before and after the flipping. Moreover, a comparison of the PMFs in the forms of free dsDNA and the AAG-dsDNA complex has pinpointed the role of AAG in discriminating εA against dA and facilitating the flipping of εA. Besides, the flipping process is simulated along the major and minor grooves, and our results have additionally demonstrated that the flipping is not directional in the free dsDNA while flipping along the major groove is kinetically more favorable than the minor groove in the AAG-dsDNA complex. Overall, our study has offered molecular insights into the flipping dynamics of εA and revealed its discrimination mechanism by AAG, which is expected to guide further enzyme engineering for therapeutic applications.
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Affiliation(s)
- Bin Liu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanping Qi
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaowei Wang
- Department of Chemical and Biological Engineering and Department of Mathematics, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon 999077, Hong Kong
| | - Xin Gao
- Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
- Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Yuan Yao
- Department of Chemical and Biological Engineering and Department of Mathematics, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon 999077, Hong Kong
| | - Lu Zhang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Fuzhou, Fujian 361005, China
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40
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Kumar S, Biswas A, Sudhakar S, Kumari D, Pradeepkumar PI. Estrone-Based Derivatives Stabilize the c-MYC and c-KIT G-Quadruplex DNA Structures. ACS OMEGA 2024; 9:6616-6626. [PMID: 38371752 PMCID: PMC10870291 DOI: 10.1021/acsomega.3c07574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 11/20/2023] [Accepted: 11/28/2023] [Indexed: 02/20/2024]
Abstract
G-rich sequences are present across the genome and can fold to form dynamic secondary structures, namely, G-quadruplexes (G4). These structures play a pivotal role in regulating numerous biological processes including replication, transcription, and translation. Therefore, targeting these structures using molecular scaffolds is an attractive approach to modulating their functions. Herein, we report the synthesis of three estrone-based derivatives (Est-1, Est-2, and Est-3) with a nonplanar core and a cationic alkyl side chain as G4 stabilizers. CD melting and polymerase stop assay results indicate that these ligands preferentially stabilize parallel c-MYC and c-KIT1 G4s over the other G4s and duplex DNAs. The ligand Est-3 shows cytotoxicity against cancer cell lines and effectively downregulates the c-KIT gene in HepG2 cell lines. Molecular modeling and dynamics studies showed that the ligand prefers stacking over the 5'-quartet of c-MYC G4 using the aromatic ring of the ligand. Overall, the findings of this study demonstrate that even G4 ligands can accommodate nonplanar scaffolds, which opens up new avenues for ligand design.
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Affiliation(s)
- Satendra Kumar
- Department of Chemistry, Indian
Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Annyesha Biswas
- 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
| | - Divya Kumari
- Department of Chemistry, Indian
Institute of Technology Bombay, Powai, Mumbai 400076, India
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41
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Kapustina AA, Tupolova YP, Popov LD, Vlasenko VG, Gishko KB, Berejnaya AG, Shcherbatykh AA, Golubeva YA, Klyushova LS, Lider EV, Lazarenko VA, Demidov OP, Knyazev PA, Bachurin SS, Nalbandyan VB, Shcherbakov IN. Copper(II) coordination compounds based on bis-hydrazones of 2,6-diacetylpyridine: synthesis, structure, and cytotoxic activity. Dalton Trans 2024; 53:3330-3347. [PMID: 38261350 DOI: 10.1039/d3dt03750a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
By reacting a series of 2,6-diacetylpyridine bis-hydrazones containing pyrimidine (H2L1), benzimidazole (H2L2) and phthalazine (H2L3) heterocyclic fragments with copper(II) chloride and bromide, a variety of pentacoordinated complexes of the composition [Cu(H2L1)X]X, [Cu(HL2)X] and [Cu(HL3)X], where X = Cl-, Br-, are formed. The properties and structure of the compounds were studied by means of NMR, IR, UV-vis, ESR, and X-ray absorption spectroscopy, cyclic voltammetry and X-Ray single crystal diffraction methods. It was shown that complexes of the cationic type [Cu(H2L1)X]X have an asymmetric structure with a distorted square-pyramidal geometry of the coordination unit. The coordination polyhedron of metal chelates [Cu(HL2)X] and [Cu(HL3)X] is an almost ideal square pyramid. Investigations of the cytotoxic activity of the obtained compounds in vitro on human hepatocellular carcinoma (HepG2) and non-tumor human lung fibroblast (MRC-5) cell lines demonstrated that complexes show higher activity compared with the well-known anticancer agent cisplatin. In addition, metal chelates [Cu(H2L1)Cl]Cl, [Cu(HL2)Cl], [Cu(HL2)Br] and [Cu(HL3)Cl] were less toxic to non-tumor cells MRC-5. A study of the binding of complexes to bovine serum albumin (BSA) protein using fluorescence spectroscopy showed that copper complexes are strongly bound to BSA. To study the mechanism of interaction of the complexes with the DNA of cancer cells, molecular dynamics simulation of the compound [Cu(HL3)Cl] was carried out. It was shown that the complex enters into π-stacking interactions predominantly with adenine and thymine bases.
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Affiliation(s)
- Anna A Kapustina
- Department of Chemistry, Southern Federal University, Rostov-on-Don, 344090, Russia.
| | - Yulia P Tupolova
- Department of Chemistry, Southern Federal University, Rostov-on-Don, 344090, Russia.
| | - Leonid D Popov
- Department of Chemistry, Southern Federal University, Rostov-on-Don, 344090, Russia.
| | - Valery G Vlasenko
- Scientific Research Institute of Physics, Southern Federal University, Rostov-on-Don, 344090, Russia
| | - Konstantin B Gishko
- Department of Chemistry, Southern Federal University, Rostov-on-Don, 344090, Russia.
| | - Alexandra G Berejnaya
- Department of Chemistry, Southern Federal University, Rostov-on-Don, 344090, Russia.
| | | | - Yuliya A Golubeva
- Nikolaev Institute of Inorganic Chemistry SB RAS, 3, Acad. Lavrentiev Ave., 630090, Novosibirsk, Russia
| | - Lyubov S Klyushova
- Institute of Molecular Biology and Biophysics, Federal Research Center of Fundamental and Translational Medicine (IMBB FRC FTM), 2/12, Timakova str., 630060, Novosibirsk, Russia
| | - Elizaveta V Lider
- Nikolaev Institute of Inorganic Chemistry SB RAS, 3, Acad. Lavrentiev Ave., 630090, Novosibirsk, Russia
| | - Vladimir A Lazarenko
- National Research Center "Kurchatov Institute", Acad. Kurchatov Sq., 1, Moscow, 123182, Russia
| | - Oleg P Demidov
- Department of Organic Chemistry, North Caucasus Federal University, Stavropol, 355017, Russia
| | - Pavel A Knyazev
- Institute of Physical and Organic Chemistry, Southern Federal University, 194/2 Stachki st, Rostov-on-Don, 344090, Russian Federation
| | - Stanislav S Bachurin
- Department of General and Clinical Biochemistry N2, Rostov State Medical University, Rostov-on-Don, 344022, Russia
| | - Vladimir B Nalbandyan
- Department of Chemistry, Southern Federal University, Rostov-on-Don, 344090, Russia.
| | - Igor N Shcherbakov
- Department of Chemistry, Southern Federal University, Rostov-on-Don, 344090, Russia.
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42
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Kaur R, Wetmore SD. Is Metal Stabilization of the Leaving Group Required or Can Lysine Facilitate Phosphodiester Bond Cleavage in Nucleic Acids? A Computational Study of EndoV. J Chem Inf Model 2024; 64:944-959. [PMID: 38253321 DOI: 10.1021/acs.jcim.3c01775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Endonuclease V (EndoV) is a single-metal-dependent enzyme that repairs deaminated DNA nucleobases in cells by cleaving the phosphodiester bond, and this enzyme has proven to be a powerful tool in biotechnology and medicine. The catalytic mechanism used by EndoV must be understood to design new disease detection and therapeutic solutions and further exploit the enzyme in interdisciplinary applications. This study has used a mixed molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) approach to compare eight distinct catalytic pathways and provides the first proposed mechanism for bacterial EndoV. The calculations demonstrate that mechanisms involving either direct or indirect metal coordination to the leaving group of the substrate previously proposed for other nucleases are unlikely for EndoV, regardless of the general base (histidine, aspartate, and substrate phosphate moiety). Instead, distinct catalytic pathways are characterized for EndoV that involve K139 stabilizing the leaving group, a metal-coordinated water stabilizing the transition structure, and either H214 or a substrate phosphate group activating the water nucleophile. In silico K139A and H214A mutational results support the newly proposed roles of these residues. Although this is a previously unseen combination of general base, general acid, and metal-binding architecture for a one-metal-dependent endonuclease, our proposed catalytic mechanisms are fully consistent with experimental kinetic, structural, and mutational data. In addition to substantiating a growing body of literature, suggesting that one metal is enough to catalyze P-O bond cleavage in nucleic acids, this new fundamental understanding of the catalytic function will promote the exploration of new and improved applications of EndoV.
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Affiliation(s)
- Rajwinder Kaur
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
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43
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Gajarsky M, Stadlbauer P, Sponer J, Cucchiarini A, Dobrovolna M, Brazda V, Mergny JL, Trantirek L, Lenarcic Zivkovic M. DNA Quadruplex Structure with a Unique Cation Dependency. Angew Chem Int Ed Engl 2024; 63:e202313226. [PMID: 38143239 DOI: 10.1002/anie.202313226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/11/2023] [Accepted: 12/22/2023] [Indexed: 12/26/2023]
Abstract
DNA quadruplex structures provide an additional layer of regulatory control in genome maintenance and gene expression and are widely used in nanotechnology. We report the discovery of an unprecedented tetrastranded structure formed from a native G-rich DNA sequence originating from the telomeric region of Caenorhabditis elegans. The structure is defined by multiple properties that distinguish it from all other known DNA quadruplexes. Most notably, the formation of a stable so-called KNa-quadruplex (KNaQ) requires concurrent coordination of K+ and Na+ ions at two distinct binding sites. This structure provides novel insight into G-rich DNA folding under ionic conditions relevant to eukaryotic cell physiology and the structural evolution of telomeric DNA. It highlights the differences between the structural organization of human and nematode telomeric DNA, which should be considered when using C. elegans as a model in telomere biology, particularly in drug screening applications. Additionally, the absence/presence of KNaQ motifs in the host/parasite introduces an intriguing possibility of exploiting the KNaQ fold as a plausible antiparasitic drug target. The structure's unique shape and ion dependency and the possibility of controlling its folding by using low-molecular-weight ligands can be used for the design or discovery of novel recognition DNA elements and sensors.
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Affiliation(s)
- Martin Gajarsky
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 753/5, 62500, Brno, Czech Republic
- Current address: Center for Molecular Medicine Cologne, University of Cologne, 50931, Cologne, Germany
| | - Petr Stadlbauer
- Institute of Biophysics, Czech Academy of Sciences, Kralovopolska 135, 61265, Brno, Czech Republic
| | - Jiri Sponer
- Institute of Biophysics, Czech Academy of Sciences, Kralovopolska 135, 61265, Brno, Czech Republic
| | - Anne Cucchiarini
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 753/5, 62500, Brno, Czech Republic
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, Inserm, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Michaela Dobrovolna
- Institute of Biophysics, Czech Academy of Sciences, Kralovopolska 135, 61265, Brno, Czech Republic
- Faculty of Chemistry, Brno University of Technology, Purkynova 464, 61200, Brno, Czech Republic
| | - Vaclav Brazda
- Institute of Biophysics, Czech Academy of Sciences, Kralovopolska 135, 61265, Brno, Czech Republic
- Faculty of Chemistry, Brno University of Technology, Purkynova 464, 61200, Brno, Czech Republic
| | - Jean-Louis Mergny
- Institute of Biophysics, Czech Academy of Sciences, Kralovopolska 135, 61265, Brno, Czech Republic
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, Inserm, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Lukas Trantirek
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 753/5, 62500, Brno, Czech Republic
| | - Martina Lenarcic Zivkovic
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 753/5, 62500, Brno, Czech Republic
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia
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44
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Brumett R, Danai L, Coffman A, Radwan Y, Teter M, Hayth H, Doe E, Pranger K, Thornburgh S, Dittmer A, Li Z, Kim TJ, Afonin KA, Khisamutdinov EF. Design and Characterization of Compact, Programmable, Multistranded Nonimmunostimulatory Nucleic Acid Nanoparticles Suitable for Biomedical Applications. Biochemistry 2024; 63:312-325. [PMID: 38271599 DOI: 10.1021/acs.biochem.3c00615] [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: 01/27/2024]
Abstract
We report a thorough investigation of the role of single-stranded thymidine (ssT) linkers in the stability and flexibility of minimal, multistranded DNA nanostructures. We systematically explore the impact of varying the number of ssTs in three-way junction motifs (3WJs) on their formation and properties. Through various UV melting experiments and molecular dynamics simulations, we demonstrate that while the number of ssTs minimally affects thermodynamic stability, the increasing ssT regions significantly enhance the structural flexibility of 3WJs. Utilizing this knowledge, we design triangular DNA nanoparticles with varying ssTs, all showing exceptional assembly efficiency except for the 0T triangle. All triangles demonstrate enhanced stability in blood serum and are nonimmunostimulatory and nontoxic in mammalian cell lines. The 4T 3WJ is chosen as the building block for constructing other polygons due to its enhanced flexibility and favorable physicochemical characteristics, making it a versatile choice for creating cost-effective, stable, and functional DNA nanostructures that can be stored in the dehydrated forms while retaining their structures. Our study provides valuable insights into the design and application of nucleic acid nanostructures, emphasizing the importance of understanding stability and flexibility in the realm of nucleic acid nanotechnology. Our findings suggest the intricate connection between these ssTs and the structural adaptability of DNA 3WJs, paving the way for more precise design and engineering of nucleic acid nanosystems suitable for broad biomedical applications.
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Affiliation(s)
- Ross Brumett
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Leyla Danai
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Abigail Coffman
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Yasmine Radwan
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Megan Teter
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Hannah Hayth
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Erwin Doe
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Katelynn Pranger
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Sable Thornburgh
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Allison Dittmer
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Zhihai Li
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Tae Jin Kim
- Department of Physical Sciences, West Virginia University Institute of Technology, Beckley, West Virginia 25801, United States
| | - Kirill A Afonin
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Emil F Khisamutdinov
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
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45
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Quraishi S, Saha D, Kumari K, Jha AN, Roy AS. Non-covalent binding interaction of bioactive coumarin esculetin with calf thymus DNA and yeast transfer RNA: A detailed investigation to decipher the binding affinities, binding location, interacting forces and structural alterations at a molecular level. Int J Biol Macromol 2024; 257:128568. [PMID: 38061533 DOI: 10.1016/j.ijbiomac.2023.128568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 11/28/2023] [Accepted: 11/30/2023] [Indexed: 01/26/2024]
Abstract
Esculetin is a well-known coumarin derivative found abundantly in nature possessing an extensive array of pharmacological and therapeutic properties. Consequently, to comprehend its molecular recognition mechanism, our objective is to conduct a complete investigation of its interactions with the nucleic acid, specifically ct-DNA, and t-RNA, using spectroscopic and computational techniques. The intrinsic fluorescence of esculetin is quenched when it interacts with ct-DNA and t-RNA, and this occurs through a static quenching mechanism. The thermodynamic parameters demonstrated that the interaction is influenced by hydrogen bonding and weak van der Waals forces. CD and FT-IR results revealed no conformational changes in ct-DNA and t-RNA structure on binding with esculetin. Furthermore, competitive displacement assay with ethidium bromide, melting temperature, viscosity measurement, and potassium iodide quenching experiments, reflected that esculetin probably binds to the minor groove of ct-DNA. The molecular docking results provided further confirmation for the spectroscopic findings, including the binding location of esculetin and binding energies of esculetin complexes with ct-DNA and t-RNA. Molecular dynamics simulation studies demonstrated the conformational stability and flexibility of nucleic acids.
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Affiliation(s)
- Sana Quraishi
- Department of Chemistry, National Institute of Technology Meghalaya, Shillong 793003, India
| | - Debanjan Saha
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur 784028, India
| | - Kalpana Kumari
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, India
| | - Anupam Nath Jha
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur 784028, India.
| | - Atanu Singha Roy
- Department of Chemistry, National Institute of Technology Meghalaya, Shillong 793003, India.
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46
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Bowleg JL, Mikek CG, Gwaltney SR. Computed interactions of berenil with restricted foldamers of c-MYC DNA G-quadruplexes. J Biomol Struct Dyn 2024; 42:2162-2169. [PMID: 37286380 DOI: 10.1080/07391102.2023.2217913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 04/16/2023] [Indexed: 06/09/2023]
Abstract
G-quadruplexes (G4s) are secondary four-stranded DNA helical structures made up of guanine-rich nucleic acids that can assemble in the promoter regions of multiple genes under the appropriate conditions. Stabilization of G4 structures by small molecules can regulate transcription in non-telomeric regions, including in proto-oncogenes and promoter regions, contributing to anti-proliferative and anti-tumor activities. Because G4s are detectable in cancer cells but not in normal cells, they make excellent drug discovery targets. Diminazene, DMZ (or berenil), has been shown to be an efficient G-quadruplex binder. Due to the stability of the folding topology, G-quadruplex structures are frequently found in the promotor regions of oncogenes and may play a regulatory role in gene activation. Using molecular docking and molecular dynamics simulations on several different binding poses, we have studied DMZ binding toward multiple G4 topologies of the c-MYC G-quadruplex. DMZ binds preferentially to G4s that have extended loops and flanking bases. This preference arises from its interactions with the loops and the flanking nucleotides, which were not found in the structure lacking extended regions. The binding to the G4s with no extended regions instead occurred mostly through end stacking. All binding sites for DMZ were confirmed by 100 ns molecular dynamics simulations and through binding enthalpies calculated using the MM-PBSA method. The primary driving forces were electrostatic, as the cationic DMZ interacts with the anionic phosphate backbone, and through van der Waals interactions, which primarily contributed in end stacking interactions.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jerrano L Bowleg
- Department of Chemistry, Mississippi State University, College Town, MS, USA
| | - Clinton G Mikek
- Department of Chemistry, Mississippi State University, College Town, MS, USA
| | - Steven R Gwaltney
- Department of Chemistry, Mississippi State University, College Town, MS, USA
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47
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Dohnalová H, Seifert M, Matoušková E, Klein M, Papini FS, Lipfert J, Dulin D, Lankaš F. Temperature-Dependent Twist of Double-Stranded RNA Probed by Magnetic Tweezer Experiments and Molecular Dynamics Simulations. J Phys Chem B 2024; 128:664-675. [PMID: 38197365 PMCID: PMC10823466 DOI: 10.1021/acs.jpcb.3c06280] [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] [Received: 09/19/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 01/11/2024]
Abstract
RNA plays critical roles in the transmission and regulation of genetic information and is increasingly used in biomedical and biotechnological applications. Functional RNAs contain extended double-stranded regions, and the structure of double-stranded RNA (dsRNA) has been revealed at high resolution. However, the dependence of the properties of the RNA double helix on environmental effects, notably temperature, is still poorly understood. Here, we use single-molecule magnetic tweezer measurements to determine the dependence of the dsRNA twist on temperature. We find that dsRNA unwinds with increasing temperature, even more than DNA, with ΔTwRNA = -14.4 ± 0.7°/(°C·kbp), compared to ΔTwDNA = -11.0 ± 1.2°/(°C·kbp). All-atom molecular dynamics (MD) simulations using a range of nucleic acid force fields, ion parameters, and water models correctly predict that dsRNA unwinds with rising temperature but significantly underestimate the magnitude of the effect. These MD data, together with additional MD simulations involving DNA and DNA-RNA hybrid duplexes, reveal a linear correlation between the twist temperature decrease and the helical rise, in line with DNA but at variance with RNA experimental data. We speculate that this discrepancy might be caused by some unknown bias in the RNA force fields tested or by as yet undiscovered transient alternative structures in the RNA duplex. Our results provide a baseline to model more complex RNA assemblies and to test and develop new parametrizations for RNA simulations. They may also inspire physical models of the temperature-dependent dsRNA structure.
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Affiliation(s)
- Hana Dohnalová
- Department
of Informatics and Chemistry, University
of Chemistry and Technology Prague, Technická 5, 166 28 Praha
6, Czech Republic
| | - Mona Seifert
- Junior
Research Group 2, Interdisciplinary Center for Clinical Research, Friedrich-Alexander-University Erlangen-Nürnberg, Cauerstr. 3, Erlangen 91058, Germany
| | - Eva Matoušková
- Department
of Informatics and Chemistry, University
of Chemistry and Technology Prague, Technická 5, 166 28 Praha
6, Czech Republic
| | - Misha Klein
- Department
of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, Amsterdam 1081 HV, The Netherlands
| | - Flávia S. Papini
- Junior
Research Group 2, Interdisciplinary Center for Clinical Research, Friedrich-Alexander-University Erlangen-Nürnberg, Cauerstr. 3, Erlangen 91058, Germany
| | - Jan Lipfert
- Soft
Condensed Matter and Biophysics, Department of Physics and Debye Institute, Utrecht University, Utrecht 3584 CC, The Netherlands
| | - David Dulin
- Junior
Research Group 2, Interdisciplinary Center for Clinical Research, Friedrich-Alexander-University Erlangen-Nürnberg, Cauerstr. 3, Erlangen 91058, Germany
- Department
of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, Amsterdam 1081 HV, The Netherlands
| | - Filip Lankaš
- Department
of Informatics and Chemistry, University
of Chemistry and Technology Prague, Technická 5, 166 28 Praha
6, Czech Republic
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48
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Love O, Winkler L, Cheatham TE. van der Waals Parameter Scanning with Amber Nucleic Acid Force Fields: Revisiting Means to Better Capture the RNA/DNA Structure through MD. J Chem Theory Comput 2024; 20:625-643. [PMID: 38157247 PMCID: PMC10809421 DOI: 10.1021/acs.jctc.3c01164] [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] [Received: 10/20/2023] [Revised: 12/11/2023] [Accepted: 12/14/2023] [Indexed: 01/03/2024]
Abstract
Molecular dynamics simulations can be used in combination with experimental techniques to uncover the intricacies of biomolecular structure, dynamics, and the resulting interactions. However, many noncanonical nucleic acid structures have proven to be challenging to replicate in accurate agreement with experimental data, often attributed to known force field deficiencies. A common force field criticism is the handling of van der Waals (vdW) parameters, which have not been updated since the regular use of Ewald's methods became routine. This work dives into the effects of minute vdW radii shifts on RNA tetranucleotide, B-DNA, and Z-DNA model systems described by commonly used Amber force fields. Using multidimensional replica exchange molecular dynamics (M-REMD), the GACC RNA tetranucleotide demonstrated changes in the structural distribution between the NMR minor and anomalous structure populations based on the O2' vdW radii scanning. However, no significant change in the NMR Major conformation population was observed. There were minimal changes in the B-DNA structure but there were more substantial improvements in Z-DNA structural descriptions, specifically with the Tumuc1 force field. This occurred with both LJbb vdW radii adjustments and incorporation of the CUFIX nonbonded parameter modifications. Though the limited vdW modifications tested did not provide a universal fix to the challenge of simulating the various known nucleic acid structures, they do provide direction and a greater understanding for future force field development efforts.
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Affiliation(s)
| | | | - 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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49
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Antolínez S, Jones PE, Phillips JC, Hadden-Perilla JA. AMBERff at Scale: Multimillion-Atom Simulations with AMBER Force Fields in NAMD. J Chem Inf Model 2024; 64:543-554. [PMID: 38176097 PMCID: PMC10806814 DOI: 10.1021/acs.jcim.3c01648] [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] [Received: 10/10/2023] [Revised: 12/18/2023] [Accepted: 12/18/2023] [Indexed: 01/06/2024]
Abstract
All-atom molecular dynamics (MD) simulations are an essential structural biology technique with increasing application to multimillion-atom systems, including viruses and cellular machinery. Classical MD simulations rely on parameter sets, such as the AMBER family of force fields (AMBERff), to accurately describe molecular motion. Here, we present an implementation of AMBERff for use in NAMD that overcomes previous limitations to enable high-performance, massively parallel simulations encompassing up to two billion atoms. Single-point potential energy comparisons and case studies on model systems demonstrate that the implementation produces results that are as accurate as running AMBERff in its native engine.
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Affiliation(s)
- Santiago Antolínez
- Department
of Chemistry and Biochemistry, University
of Delaware, Newark, Delaware 19716, United States
| | - Peter Eugene Jones
- Department
of Chemistry and Biochemistry, University
of Delaware, Newark, Delaware 19716, United States
| | - James C. Phillips
- National
Center for Supercomputing Applications, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Jodi A. Hadden-Perilla
- Department
of Chemistry and Biochemistry, University
of Delaware, Newark, Delaware 19716, United States
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50
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Zhen X, Xu X, Ye L, Xie S, Huang Z, Yang S, Wang Y, Li J, Long F, Ouyang S. Structural basis of antiphage immunity generated by a prokaryotic Argonaute-associated SPARSA system. Nat Commun 2024; 15:450. [PMID: 38200015 PMCID: PMC10781750 DOI: 10.1038/s41467-023-44660-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 12/26/2023] [Indexed: 01/12/2024] Open
Abstract
Argonaute (Ago) proteins are ubiquitous across all kingdoms of life. Eukaryotic Agos (eAgos) use small RNAs to recognize transcripts for RNA silencing in eukaryotes. In contrast, the functions of prokaryotic counterparts (pAgo) are less well known. Recently, short pAgos in conjunction with the associated TIR or Sir2 (SPARTA or SPARSA) were found to serve as antiviral systems to combat phage infections. Herein, we present the cryo-EM structures of nicotinamide adenine dinucleotide (NAD+)-bound SPARSA with and without nucleic acids at resolutions of 3.1 Å and 3.6 Å, respectively. Our results reveal that the APAZ (Analogue of PAZ) domain and the short pAgo form a featured architecture similar to the long pAgo to accommodate nucleic acids. We further identified the key residues for NAD+ binding and elucidated the structural basis for guide RNA and target DNA recognition. Using structural comparisons, molecular dynamics simulations, and biochemical experiments, we proposed a putative mechanism for NAD+ hydrolysis in which an H186 loop mediates nucleophilic attack by catalytic water molecules. Overall, our study provides mechanistic insight into the antiphage role of the SPARSA system.
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Affiliation(s)
- Xiangkai Zhen
- Key Laboratory of Microbial Pathogenesis and Interventions of Fujian Province University, the Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China
| | - Xiaolong Xu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China Wuhan University, Wuhan, 430071, China
| | - Le Ye
- Key Laboratory of Microbial Pathogenesis and Interventions of Fujian Province University, the Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China
| | - Song Xie
- College of Chemistry, Fuzhou University, 350116, Fuzhou, China
| | - Zhijie Huang
- Key Laboratory of Microbial Pathogenesis and Interventions of Fujian Province University, the Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China
| | - Sheng Yang
- Key Laboratory of Microbial Pathogenesis and Interventions of Fujian Province University, the Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China
| | - Yanhui Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China Wuhan University, Wuhan, 430071, China
| | - Jinyu Li
- College of Chemistry, Fuzhou University, 350116, Fuzhou, China.
| | - Feng Long
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China Wuhan University, Wuhan, 430071, China.
| | - Songying Ouyang
- Key Laboratory of Microbial Pathogenesis and Interventions of Fujian Province University, the Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China.
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