1
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Cioccolo S, Barritt JD, Pollock N, Hall Z, Babuta J, Sridhar P, Just A, Morgner N, Dafforn T, Gould I, Byrne B. The mycobacterium lipid transporter MmpL3 is dimeric in detergent solution, SMALPs and reconstituted nanodiscs. RSC Chem Biol 2024; 5:901-913. [PMID: 39211474 PMCID: PMC11352979 DOI: 10.1039/d4cb00110a] [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: 05/21/2024] [Accepted: 07/26/2024] [Indexed: 09/04/2024] Open
Abstract
The mycobacterial membrane protein large 3 (MmpL3) transports key precursor lipids to the outer membrane of Mycobacterium species. Multiple structures of MmpL3 from both M. tuberculosis and M. smegmatis in various conformational states indicate that the protein is both structurally and functionally monomeric. However, most other resistance, nodulation and cell division (RND) transporters structurally characterised to date are either dimeric or trimeric. Here we present an in depth biophysical and computational analysis revealing that MmpL3 from M. smegmatis exists as a dimer in a variety of membrane mimetic systems (SMALPs, detergent-based solution and nanodiscs). Sucrose gradient separation of MmpL3 populations from M. smegmatis, reconstituted into nanodiscs, identified monomeric and dimeric populations of the protein using laser induced liquid bead ion desorption (LILBID), a native mass spectrometry technique. Preliminary cryo-EM analysis confirmed that MmpL3 forms physiological dimers. Untargeted lipidomics experiments on membrane protein co-purified lipids revealed PE and PG lipid classes were predominant. Molecular dynamics (MD) simulations, in the presence of physiologically-relevant lipid compositions revealed the likely dimer interface.
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Affiliation(s)
- Sara Cioccolo
- Department of Life Sciences, Imperial College London Exhibition Road, South Kensington London SW7 2AZ UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London Shepherd's Bush London W12 0BZ UK
| | - Joseph D Barritt
- Department of Life Sciences, Imperial College London Exhibition Road, South Kensington London SW7 2AZ UK
| | - Naomi Pollock
- School of Biosciences, University of Birmingham Birmingham UK
| | - Zoe Hall
- Division of Systems Medicine, Imperial College London London UK
| | - Julia Babuta
- Division of Systems Medicine, Imperial College London London UK
| | - Pooja Sridhar
- School of Biosciences, University of Birmingham Birmingham UK
| | - Alicia Just
- Institute of Physical and Theoretical Chemistry, J.W. Goethe-University Frankfurt am Main Germany
| | - Nina Morgner
- Institute of Physical and Theoretical Chemistry, J.W. Goethe-University Frankfurt am Main Germany
| | - Tim Dafforn
- School of Biosciences, University of Birmingham Birmingham UK
| | - Ian Gould
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London Shepherd's Bush London W12 0BZ UK
| | - Bernadette Byrne
- Department of Life Sciences, Imperial College London Exhibition Road, South Kensington London SW7 2AZ UK
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2
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Gomes DEB, Yang B, Vanella R, Nash MA, Bernardi RC. Integrating Dynamic Network Analysis with AI for Enhanced Epitope Prediction in PD-L1:Affibody Interactions. J Am Chem Soc 2024; 146:23842-23853. [PMID: 39146039 DOI: 10.1021/jacs.4c05869] [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: 08/17/2024]
Abstract
Understanding binding epitopes involved in protein-protein interactions and accurately determining their structure are long-standing goals with broad applicability in industry and biomedicine. Although various experimental methods for binding epitope determination exist, these approaches are typically low throughput and cost-intensive. Computational methods have potential to accelerate epitope predictions; however, recently developed artificial intelligence (AI)-based methods frequently fail to predict epitopes of synthetic binding domains with few natural homologues. Here we have developed an integrated method employing generalized-correlation-based dynamic network analysis on multiple molecular dynamics (MD) trajectories, initiated from AlphaFold2Multimer structures, to unravel the structure and binding epitope of the therapeutic PD-L1:Affibody complex. Both AlphaFold2 and conventional molecular dynamics trajectory analysis were ineffective in distinguishing between two proposed binding models, parallel and perpendicular. However, our integrated approach, utilizing dynamic network analysis, demonstrated that the perpendicular mode was significantly more stable. These predictions were validated using a suite of experimental epitope mapping protocols, including cross-linking mass spectrometry and next-generation sequencing-based deep mutational scanning. Conversely, AlphaFold3 failed to predict a structure bound in the perpendicular pose, highlighting the necessity for exploratory research in the search for binding epitopes and challenging the notion that AI-generated protein structures can be accepted without scrutiny. Our research underscores the potential of employing dynamic network analysis to enhance AI-based structure predictions for more accurate identification of protein-protein interaction interfaces.
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Affiliation(s)
- Diego E B Gomes
- Department of Physics, Auburn University, Auburn, Alabama 36849, United States
| | - Byeongseon Yang
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, Basel 4058, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
| | - Rosario Vanella
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, Basel 4058, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
| | - Michael A Nash
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, Basel 4058, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
| | - Rafael C Bernardi
- Department of Physics, Auburn University, Auburn, Alabama 36849, United States
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3
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Carrasco JL, Ambrós S, Gutiérrez PA, Elena SF. Adaptation of turnip mosaic virus to Arabidopsis thaliana involves rewiring of VPg-host proteome interactions. Virus Evol 2024; 10:veae055. [PMID: 39091990 PMCID: PMC11291303 DOI: 10.1093/ve/veae055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 05/23/2024] [Accepted: 07/16/2024] [Indexed: 08/04/2024] Open
Abstract
The outcome of a viral infection depends on a complex interplay between the host physiology and the virus, mediated through numerous protein-protein interactions. In a previous study, we used high-throughput yeast two-hybrid (HT-Y2H) to identify proteins in Arabidopsis thaliana that bind to the proteins encoded by the turnip mosaic virus (TuMV) genome. Furthermore, after experimental evolution of TuMV lineages in plants with mutations in defense-related or proviral genes, most mutations observed in the evolved viruses affected the VPg cistron. Among these mutations, D113G was a convergent mutation selected in many lineages across different plant genotypes, including cpr5-2 with constitutive expression of systemic acquired resistance. In contrast, mutation R118H specifically emerged in the jin1 mutant with affected jasmonate signaling. Using the HT-Y2H system, we analyzed the impact of these two mutations on VPg's interaction with plant proteins. Interestingly, both mutations severely compromised the interaction of VPg with the translation initiation factor eIF(iso)4E, a crucial interactor for potyvirus infection. Moreover, mutation D113G, but not R118H, adversely affected the interaction with RHD1, a zinc-finger homeodomain transcription factor involved in regulating DNA demethylation. Our results suggest that RHD1 enhances plant tolerance to TuMV infection. We also discuss our findings in a broad virus evolution context.
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Affiliation(s)
- José L Carrasco
- Instituto de Biología Integrativa de Sistemas (CSIC—Universitat de València), Catedratico Agustin Escardino 9, Paterna, València 46182, Spain
| | - Silvia Ambrós
- Instituto de Biología Integrativa de Sistemas (CSIC—Universitat de València), Catedratico Agustin Escardino 9, Paterna, València 46182, Spain
| | - Pablo A Gutiérrez
- Laboratorio de Microbiología Industrial, Facultad de Ciencias, Universidad Nacional de Colombia, Carrera 65 Nro. 59A - 110, Medellín, Antioquia 050034, Colombia
| | - Santiago F Elena
- Instituto de Biología Integrativa de Sistemas (CSIC—Universitat de València), Catedratico Agustin Escardino 9, Paterna, València 46182, Spain
- The Santa Fe Institute, 1399 Hyde Park Rd, Santa Fe, NM 87501, United States
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4
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Zeng Y, Pavlova A, Nelson PM, Glick ZL, Yang L, Pang YT, Spivak M, Licari G, Tajkhorshid E, Sherrill CD, Gumbart JC. Broadening access to small-molecule parameterization with the force field toolkit. J Chem Phys 2024; 160:242501. [PMID: 38916266 DOI: 10.1063/5.0196848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 05/27/2024] [Indexed: 06/26/2024] Open
Abstract
Access to accurate force-field parameters for small molecules is crucial for computational studies of their interactions with proteins. Although a number of general force fields for small molecules exist, e.g., CGenFF, GAFF, and OPLS, they do not cover all common chemical groups and their combinations. The Force Field Toolkit (ffTK) provides a comprehensive graphical interface that streamlines the development of classical parameters for small molecules directly from quantum mechanical (QM) calculations, allowing for force-field generation for almost any chemical group and validation of the fit relative to the target data. ffTK relies on supported external software for the QM calculations, but it can generate the necessary QM input files and parse and analyze the QM output. In previous ffTK versions, support for Gaussian and ORCA QM packages was implemented. Here, we add support for Psi4, an open-source QM package free for all users, thereby broadening user access to ffTK. We also compare the parameter sets obtained with the new ffTK version using Gaussian, ORCA, and Psi4 for three molecules: pyrrolidine, n-propylammonium cation, and chlorobenzene. Despite minor differences between the resulting parameter sets for each compound, most prominently in the dihedral and improper terms, we show that conformational distributions sampled in molecular dynamics simulations using these parameter sets are quite comparable.
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Affiliation(s)
- Yunlin Zeng
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Anna Pavlova
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Philip M Nelson
- Center for Computational Molecular Science and Technology, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
- School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Zachary L Glick
- Center for Computational Molecular Science and Technology, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
- School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Lan Yang
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Yui Tik Pang
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Mariano Spivak
- Theoretical and Computational Biophysics Group, NIH Resource for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Giuseppe Licari
- Theoretical and Computational Biophysics Group, NIH Resource for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Resource for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Biochemistry and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - C David Sherrill
- Center for Computational Molecular Science and Technology, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
- School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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5
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Tortora F, Guerrera V, Lettieri G, Febbraio F, Piscopo M. Prediction of Pesticide Interactions with Proteins Involved in Human Reproduction by Using a Virtual Screening Approach: A Case Study of Famoxadone Binding CRBP-III and Izumo. Int J Mol Sci 2024; 25:5790. [PMID: 38891976 PMCID: PMC11171824 DOI: 10.3390/ijms25115790] [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: 05/07/2024] [Revised: 05/21/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024] Open
Abstract
In recent years, the awareness that pesticides can have other effects apart from generic toxicity is growing. In particular, several pieces of evidence highlight their influence on human fertility. In this study, we investigated, by a virtual screening approach, the binding between pesticides and proteins present in human gametes or associated with reproduction, in order to identify new interactions that could affect human fertility. To this aim, we prepared ligand (pesticides) and receptor (proteins) 3D structure datasets from online structural databases (such as PubChem and RCSB), and performed a virtual screening analysis using Autodock Vina. In the comparison of the predicted interactions, we found that famoxadone was predicted to bind Cellular Retinol Binding Protein-III in the retinol-binding site with a better minimum energy value of -10.4 Kcal/mol and an RMSD of 3.77 with respect to retinol (-7.1 Kcal/mol). In addition to a similar network of interactions, famoxadone binding is more stabilized by additional hydrophobic patches including L20, V29, A33, F57, L117, and L118 amino acid residues and hydrogen bonds with Y19 and K40. These results support a possible competitive effect of famoxadone on retinol binding with impacts on the ability of developing the cardiac tissue, in accordance with the literature data on zebrafish embryos. Moreover, famoxadone binds, with a minimum energy value between -8.3 and -8.0 Kcal/mol, to the IZUMO Sperm-Egg Fusion Protein, interacting with a network of polar and hydrophobic amino acid residues in the cavity between the 4HB and Ig-like domains. This binding is more stabilized by a predicted hydrogen bond with the N185 residue of the protein. A hindrance in this position can probably affect the conformational change for JUNO binding, avoiding the gamete membrane fusion to form the zygote. This work opens new interesting perspectives of study on the effects of pesticides on fertility, extending the knowledge to other typologies of interaction which can affect different steps of the reproductive process.
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Affiliation(s)
- Fabiana Tortora
- Institute of Genetics and Biophysics “Adriano Buzzati Traverso”, National Research Council (CNR), Via P. Castellino 111, 80131 Naples, Italy;
- Institute of Biochemistry and Cell Biology, National Research Council (CNR), Via P. Castellino 111, 80131 Naples, Italy
| | - Valentina Guerrera
- Institute of Biochemistry and Cell Biology, National Research Council (CNR), Via P. Castellino 111, 80131 Naples, Italy
| | - Gennaro Lettieri
- Department of Biology, University of Naples Federico II, Via Cinthia, 21, 80126 Naples, Italy (M.P.)
| | - Ferdinando Febbraio
- Institute of Biochemistry and Cell Biology, National Research Council (CNR), Via P. Castellino 111, 80131 Naples, Italy
| | - Marina Piscopo
- Department of Biology, University of Naples Federico II, Via Cinthia, 21, 80126 Naples, Italy (M.P.)
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6
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Doga H, Raubenolt B, Cumbo F, Joshi J, DiFilippo FP, Qin J, Blankenberg D, Shehab O. A Perspective on Protein Structure Prediction Using Quantum Computers. J Chem Theory Comput 2024; 20:3359-3378. [PMID: 38703105 PMCID: PMC11099973 DOI: 10.1021/acs.jctc.4c00067] [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: 01/22/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 05/06/2024]
Abstract
Despite the recent advancements by deep learning methods such as AlphaFold2, in silico protein structure prediction remains a challenging problem in biomedical research. With the rapid evolution of quantum computing, it is natural to ask whether quantum computers can offer some meaningful benefits for approaching this problem. Yet, identifying specific problem instances amenable to quantum advantage and estimating the quantum resources required are equally challenging tasks. Here, we share our perspective on how to create a framework for systematically selecting protein structure prediction problems that are amenable for quantum advantage, and estimate quantum resources for such problems on a utility-scale quantum computer. As a proof-of-concept, we validate our problem selection framework by accurately predicting the structure of a catalytic loop of the Zika Virus NS3 Helicase, on quantum hardware.
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Affiliation(s)
- Hakan Doga
- IBM Quantum,
Almaden Research Center, San Jose, California 95120, United States
| | - Bryan Raubenolt
- Center
for Computational Life Sciences, Lerner
Research Institute, The Cleveland Clinic, Cleveland, Ohio 44106, United States
| | - Fabio Cumbo
- Center
for Computational Life Sciences, Lerner
Research Institute, The Cleveland Clinic, Cleveland, Ohio 44106, United States
| | - Jayadev Joshi
- Center
for Computational Life Sciences, Lerner
Research Institute, The Cleveland Clinic, Cleveland, Ohio 44106, United States
| | - Frank P. DiFilippo
- Center
for Computational Life Sciences, Lerner
Research Institute, The Cleveland Clinic, Cleveland, Ohio 44106, United States
| | - Jun Qin
- Center
for Computational Life Sciences, Lerner
Research Institute, The Cleveland Clinic, Cleveland, Ohio 44106, United States
| | - Daniel Blankenberg
- Center
for Computational Life Sciences, Lerner
Research Institute, The Cleveland Clinic, Cleveland, Ohio 44106, United States
| | - Omar Shehab
- IBM
Quantum, IBM Thomas J Watson Research Center, Yorktown Heights, New York 10598, United States
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7
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Zhang R, Huang L, Zhang X, Yu Y, Liang T, Wang H, Zhang X, Hu D, Wang B, Wang Y, Jiang J, Yu X. Proteomics Platform Reveals Broad-Spectrum Nanobodies for SARS-CoV-2 Variant Neutralization. J Proteome Res 2024; 23:1559-1570. [PMID: 38603467 DOI: 10.1021/acs.jproteome.3c00569] [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: 04/13/2024]
Abstract
The ongoing evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to the emergence of different variants of concerns with immune evasion that have been prevalent over the past three years. Nanobodies, the functional variable regions of camelid heavy-chain-only antibodies, have garnered interest in developing neutralizing antibodies due to their smaller size, structural stability, ease of production, high affinity, and low immunogenicity, among other characteristics. In this work, we describe an integrated proteomics platform for the high-throughput screening of nanobodies against different SARS-CoV-2 spike variants. To demonstrate this platform, we immunized a camel with subunit 1 (S1) of the wild-type spike protein and constructed a nanobody phage library. The binding and neutralizing activities of the nanobodies against 72 spike variants were then measured, resulting in the identification of two nanobodies (C-282 and C-39) with broad neutralizing activity against six non-Omicron variants (D614G, Alpha, Beta, Gamma, Delta, Kappa) and five Omicron variants (BA.1-5). Their neutralizing capability was validated using in vitro pseudovirus-based neutralization assays. All these results demonstrate the utility of our proteomics platform to identify new nanobodies with broad neutralizing capability and to develop a treatment for patients with SARS-CoV-2 variant infection in the future.
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Affiliation(s)
- Ran Zhang
- School of Basic Medicine Sciences, Anhui Medical University, Hefei, Anhui 230031, PR China
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Lan Huang
- Changping Laboratory, Beijing 102206, China
| | - Xiaohan Zhang
- School of Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | | | - Te Liang
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Hongye Wang
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Xiaomei Zhang
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Di Hu
- ProteomicsEra Medical Co., Ltd., Beijing 102206, China
| | - Bingwei Wang
- School of Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | | | - Junyi Jiang
- Translational Medicine Technology Platform, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Xiaobo Yu
- School of Basic Medicine Sciences, Anhui Medical University, Hefei, Anhui 230031, PR China
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
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8
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Chang Z, Ma C, Wang R, Wang B, Yang M, Li B, Zhang T, Li Z, Zhao P, Qi X, Wang J. Design and Mechanism Study of High-Safety and Long-Life Electrolyte for High-Energy-Density Lithium-Ion Batteries. ACS APPLIED MATERIALS & INTERFACES 2024; 16:18980-18990. [PMID: 38577916 DOI: 10.1021/acsami.4c02237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
Although nonflammable electrolytes are beneficial for battery safety, they often adversely affect the electrochemical performance of lithium-ion batteries due to their poor compatibility with electrodes. Herein, we design a nonflammable electrolyte consisting of cyclic carbonate and 2,2-difluoroethyl acetate (DFEA) solvents paired with several surface-film-forming additives, significantly improving the safety and cycling performance of NMC811||SiOx/graphite pouch cells. The DFEA solvent exhibits not only good flame retardancy but also lower lowest unoccupied molecular orbital (LUMO) energy, promoting the formation of a robust inorganic-rich and gradient-architecture hybrid interface between the SiOx/graphite anode and electrolyte. The double insurance of good flame retardancy of the DFEA solvent and decreased exothermic effects of both bulk electrolyte and DFEA-derived solid electrolyte interphase (SEI) can ensure the high safety of the pouch cell. Moreover, the highly robust SEI can prevent the excessive reduction decomposition of the electrolyte and alleviate the structural decay of the anode, which can restrain the formation of lithium deposition on the anode surface and further suppress the structural decay of NMC materials. This contributes to the unprecedented cycling performance of the NMC811||SiOx/graphite pouch cells with a capacity retention of 80% after 1000 cycles at a 0.33C rate.
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Affiliation(s)
- Zenghua Chang
- China Automotive Battery Research Institute Co., Ltd., No. 11 Xingke Dong Street, Huairou District, Beijing 101407, P. R. China
- General Research Institute for Nonferrous Metals, No. 2 Xinjiekou Wai Street, Xicheng District, Beijing 100088, P. R. China
- National Power Battery Innovation Center, GRINM Group Corporation Limited (GRINM Group), No. 2 Xinjiekou Wai Street, Xicheng District, Beijing 100088, P. R. China
| | - Chenxi Ma
- China Automotive Battery Research Institute Co., Ltd., No. 11 Xingke Dong Street, Huairou District, Beijing 101407, P. R. China
- National Power Battery Innovation Center, GRINM Group Corporation Limited (GRINM Group), No. 2 Xinjiekou Wai Street, Xicheng District, Beijing 100088, P. R. China
| | - Rennian Wang
- China Automotive Battery Research Institute Co., Ltd., No. 11 Xingke Dong Street, Huairou District, Beijing 101407, P. R. China
- National Power Battery Innovation Center, GRINM Group Corporation Limited (GRINM Group), No. 2 Xinjiekou Wai Street, Xicheng District, Beijing 100088, P. R. China
| | - Bo Wang
- China Automotive Battery Research Institute Co., Ltd., No. 11 Xingke Dong Street, Huairou District, Beijing 101407, P. R. China
- National Power Battery Innovation Center, GRINM Group Corporation Limited (GRINM Group), No. 2 Xinjiekou Wai Street, Xicheng District, Beijing 100088, P. R. China
| | - Man Yang
- China Automotive Battery Research Institute Co., Ltd., No. 11 Xingke Dong Street, Huairou District, Beijing 101407, P. R. China
- General Research Institute for Nonferrous Metals, No. 2 Xinjiekou Wai Street, Xicheng District, Beijing 100088, P. R. China
- National Power Battery Innovation Center, GRINM Group Corporation Limited (GRINM Group), No. 2 Xinjiekou Wai Street, Xicheng District, Beijing 100088, P. R. China
| | - Bin Li
- China Automotive Battery Research Institute Co., Ltd., No. 11 Xingke Dong Street, Huairou District, Beijing 101407, P. R. China
- National Power Battery Innovation Center, GRINM Group Corporation Limited (GRINM Group), No. 2 Xinjiekou Wai Street, Xicheng District, Beijing 100088, P. R. China
| | - Tianhang Zhang
- China Automotive Battery Research Institute Co., Ltd., No. 11 Xingke Dong Street, Huairou District, Beijing 101407, P. R. China
- General Research Institute for Nonferrous Metals, No. 2 Xinjiekou Wai Street, Xicheng District, Beijing 100088, P. R. China
- National Power Battery Innovation Center, GRINM Group Corporation Limited (GRINM Group), No. 2 Xinjiekou Wai Street, Xicheng District, Beijing 100088, P. R. China
| | - Zhanhai Li
- China Automotive Battery Research Institute Co., Ltd., No. 11 Xingke Dong Street, Huairou District, Beijing 101407, P. R. China
- National Power Battery Innovation Center, GRINM Group Corporation Limited (GRINM Group), No. 2 Xinjiekou Wai Street, Xicheng District, Beijing 100088, P. R. China
| | - Peizhu Zhao
- China Automotive Battery Research Institute Co., Ltd., No. 11 Xingke Dong Street, Huairou District, Beijing 101407, P. R. China
- National Power Battery Innovation Center, GRINM Group Corporation Limited (GRINM Group), No. 2 Xinjiekou Wai Street, Xicheng District, Beijing 100088, P. R. China
| | - Xiaopeng Qi
- China Automotive Battery Research Institute Co., Ltd., No. 11 Xingke Dong Street, Huairou District, Beijing 101407, P. R. China
- General Research Institute for Nonferrous Metals, No. 2 Xinjiekou Wai Street, Xicheng District, Beijing 100088, P. R. China
- National Power Battery Innovation Center, GRINM Group Corporation Limited (GRINM Group), No. 2 Xinjiekou Wai Street, Xicheng District, Beijing 100088, P. R. China
| | - Jiantao Wang
- China Automotive Battery Research Institute Co., Ltd., No. 11 Xingke Dong Street, Huairou District, Beijing 101407, P. R. China
- General Research Institute for Nonferrous Metals, No. 2 Xinjiekou Wai Street, Xicheng District, Beijing 100088, P. R. China
- National Power Battery Innovation Center, GRINM Group Corporation Limited (GRINM Group), No. 2 Xinjiekou Wai Street, Xicheng District, Beijing 100088, P. R. China
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9
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Ismail CMKH, Abdul Hamid AA, Abdul Rashid NN, Lestari W, Mokhtar KI, Mustafa Alahmad BE, Abd Razak MRM, Ismail A. An ensemble docking-based virtual screening and molecular dynamics simulation of phytochemical compounds from Malaysian Kelulut Honey (KH) against SARS-CoV-2 target enzyme, human angiotensin-converting enzyme 2 (ACE-2). J Biomol Struct Dyn 2024:1-30. [PMID: 38279932 DOI: 10.1080/07391102.2024.2308762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 01/17/2024] [Indexed: 01/29/2024]
Abstract
The human angiotensin-converting enzyme 2 (ACE-2) receptor is a metalloenzyme that plays an important role in regulating blood pressure by modulating angiotensin II. This receptor facilitates SARS-CoV-2 entry into human cells via receptor-mediated endocytosis, causing the global COVID-19 pandemic and a major health crisis. Kelulut honey (KH), one of Malaysian honey recently gained attention for its distinct flavour and taste while having many nutritional and medicinal properties. Recent study demonstrates the antiviral potential of KH against SARS-CoV-2 by inhibiting ACE-2 in vitro, but the bioactive compound pertaining to the ACE-2 inhibition is yet unknown. An ensemble docking-based virtual screening was employed to screen the phytochemical compounds from KH with high binding affinity against the 10 best representative structures of ACE-2 that mostly formed from MD simulation. From 110 phytochemicals previously identified in KH, 27 compounds passed the ADMET analysis and proceeded to docking. Among the docked compound, SDC and FMN consistently exhibited strong binding to ACE-2's active site (-9.719 and -9.473 kcal/mol) and allosteric site (-7.305 and -7.464 kcal/mol) as compared to potent ACE-2 inhibitor, MLN 4760. Detailed trajectory analysis of MD simulation showed stable binding interaction towards active and allosteric sites of ACE-2. KH's compounds show promise in inhibiting SARS-CoV-2 binding to ACE-2 receptors, indicating potential for preventive use or as a supplement to other COVID-19 treatments. Additional research is needed to confirm KH's antiviral effects and its role in SARS-CoV-2 therapy, including prophylaxis and adjuvant treatment with vaccination.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Che Muhammad Khairul Hisyam Ismail
- Department of Biotechnology, Kulliyyah of Science, International Islamic University Malaysia, Kuantan, Pahang, Malaysia
- Research Unit for Bioinformatics & Computational Biology (RUBIC), Kulliyyah of Science, International Islamic University Malaysia, Kuantan, Pahang, Malaysia
| | - Azzmer Azzar Abdul Hamid
- Department of Biotechnology, Kulliyyah of Science, International Islamic University Malaysia, Kuantan, Pahang, Malaysia
- Research Unit for Bioinformatics & Computational Biology (RUBIC), Kulliyyah of Science, International Islamic University Malaysia, Kuantan, Pahang, Malaysia
| | | | - Widya Lestari
- Department of Fundamental Dental and Medical Sciences, Kulliyyah of Dentistry, International Islamic University Malaysia, Kuantan, Pahang, Malaysia
| | - Khairani Idah Mokhtar
- Department of Fundamental Dental and Medical Sciences, Kulliyyah of Dentistry, International Islamic University Malaysia, Kuantan, Pahang, Malaysia
| | - Basma Ezzat Mustafa Alahmad
- Department of Fundamental Dental and Medical Sciences, Kulliyyah of Dentistry, International Islamic University Malaysia, Kuantan, Pahang, Malaysia
| | - Mohd Ridzuan Mohd Abd Razak
- Herbal Medicine Research Centre, Institute for Medical Research, National Institutes of Health, Shah Alam, Selangor, Malaysia
| | - Azlini Ismail
- Department of Fundamental Dental and Medical Sciences, Kulliyyah of Dentistry, International Islamic University Malaysia, Kuantan, Pahang, Malaysia
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Kim MJ, Martin CA, Kim J, Jablonski MM. Computational methods in glaucoma research: Current status and future outlook. Mol Aspects Med 2023; 94:101222. [PMID: 37925783 PMCID: PMC10842846 DOI: 10.1016/j.mam.2023.101222] [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: 08/01/2023] [Revised: 10/06/2023] [Accepted: 10/19/2023] [Indexed: 11/07/2023]
Abstract
Advancements in computational techniques have transformed glaucoma research, providing a deeper understanding of genetics, disease mechanisms, and potential therapeutic targets. Systems genetics integrates genomic and clinical data, aiding in identifying drug targets, comprehending disease mechanisms, and personalizing treatment strategies for glaucoma. Molecular dynamics simulations offer valuable molecular-level insights into glaucoma-related biomolecule behavior and drug interactions, guiding experimental studies and drug discovery efforts. Artificial intelligence (AI) technologies hold promise in revolutionizing glaucoma research, enhancing disease diagnosis, target identification, and drug candidate selection. The generalized protocols for systems genetics, MD simulations, and AI model development are included as a guide for glaucoma researchers. These computational methods, however, are not separate and work harmoniously together to discover novel ways to combat glaucoma. Ongoing research and progresses in genomics technologies, MD simulations, and AI methodologies project computational methods to become an integral part of glaucoma research in the future.
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Affiliation(s)
- Minjae J Kim
- Department of Ophthalmology, The Hamilton Eye Institute, The University of Tennessee Health Science Center, Memphis, TN, 38163, USA.
| | - Cole A Martin
- Department of Ophthalmology, The Hamilton Eye Institute, The University of Tennessee Health Science Center, Memphis, TN, 38163, USA.
| | - Jinhwa Kim
- Graduate School of Artificial Intelligence, Graduate School of Metaverse, Department of Management Information Systems, Sogang University, 1 Shinsoo-Dong, Mapo-Gu, Seoul, South Korea.
| | - Monica M Jablonski
- Department of Ophthalmology, The Hamilton Eye Institute, The University of Tennessee Health Science Center, Memphis, TN, 38163, USA.
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Guo Y, Guo Y, Guo Z, Liu B, Xu J. Effect of Fragment 1 on the Binding of Epigallocatechin Gallate to the PD-L1 Dimer Explored by Molecular Dynamics. Molecules 2023; 28:7881. [PMID: 38067610 PMCID: PMC10708077 DOI: 10.3390/molecules28237881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 11/28/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
Blocking the interaction between programmed cell death-1 (PD-1) and programmed cell death-ligand 1 (PD-L1) by directly targeting the PD-L1 dimer has emerged as a hot topic in the field of cancer immunotherapy. Epigallocatechin gallate (EGCG), a natural product, has been demonstrated binding to the PD-L1 dimer in our previous study, but has a weaker binding capacity, moreover, EGCG is located at the end of the binding pocket of the PD-L1 dimer. The inhibitor fragment 1 (FRA) lies at the other end. So, we proposed that the introduction of FRA might be able to improve the binding ability. To illuminate this issue, molecular dynamics (MD) simulation was performed in the present study. Binding free energy calculations show that the binding affinity is significantly increased by 17 kcal/mol upon the introduction of FRA. It may be due to the energy contributions of emerging key residues ATyr56, AMet115, BTyr123, AIle54 and the enhanced contributions of initial key residues ATyr123 and BVal68. Binding mode and non-bonded interaction results indicate that FRA_EGCG (EGCG in combination with FRA) binds to the C-, F- and G-sheet of the PD-L1 dimer. Importantly, the introduction of FRA mainly strengthened the nonpolar interactions. The free energy landscape and secondary structure results further show that FRA_EGCG can interact with the PD-L1 dimer more stably. These data demonstrated here provide the theoretical basis for screening two or more natural products with additive inhibitory effect on this pathway and therefore exerting more effective anticancer immunity.
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Affiliation(s)
- Yan Guo
- College of Food Science, Shanxi Normal University, Taiyuan 030031, China; (Y.G.); (Y.G.); (Z.G.)
| | - Yilin Guo
- College of Food Science, Shanxi Normal University, Taiyuan 030031, China; (Y.G.); (Y.G.); (Z.G.)
| | - Zichao Guo
- College of Food Science, Shanxi Normal University, Taiyuan 030031, China; (Y.G.); (Y.G.); (Z.G.)
| | - Boping Liu
- Key Laboratory for Bio-Based Materials and Energy of Ministry of Education, College of Materials and Energy, South China Agricultural University, Guangzhou 510630, China
| | - Jianguo Xu
- College of Food Science, Shanxi Normal University, Taiyuan 030031, China; (Y.G.); (Y.G.); (Z.G.)
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