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Ruiz-Castelan JE, Villa-Díaz F, Castro ME, Melendez FJ, Scior T. The α/β3 complex of human voltage-gated sodium channel hNa v1.7 to study mechanistic differences in presence and absence of auxiliary subunit β3. J Mol Model 2025; 31:168. [PMID: 40397258 PMCID: PMC12095431 DOI: 10.1007/s00894-025-06378-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2024] [Accepted: 04/25/2025] [Indexed: 05/22/2025]
Abstract
CONTEXT In the context of structural interactomics, we generated a 3D model between α and β3 subunits for the hitherto unknown human voltage-gated sodium channel complex (hNa 1.7α/β3). We embedded our 3D model in a membrane lipid bilayer for molecular dynamics (MD) simulations of the sodium cation passage from the outer vestibule through the inner pore segment of our hNa 1.7 complex in presence and absence of auxiliary subunit β3 with remarkable changes close to electrophysiological study results. A complete passage could not be expected due to because the inactivated state of the underlying 3D template. A complete sodium ion passage would require an open state of the channel. The computed observations concerning side chain rearrangements for favorable cooperativity under evolutionary neighborhood conditions, favorable and unfavorable amino acid interactions, proline kink, loop, and helix displacements were all found in excellent keeping with the extant literature without any exception nor contradiction. Complex-stabilizing pairs of interacting amino acids with evolutionary neighborhood complementary were identified. METHODS The following tools were used: sequence search and alignment by FASTA and Clustal Omega; 3D model visualization and homology modeling by Vega ZZ, SPDBV, Chimera and Modeller, respectively; missing sections (loops) by Alphafold; geometry optimization prior to MD runs by GROMACS 2021.4 under the CHARMM 36 force field; local healing of bad contacts by SPDBV based on its Ramachandran plots; protein-protein docking by HDOCK 2.4; membrane insertion assisted by OPM; Berendsen V-rescaling for NVT; Parrinello-Rahman and Nose-Hoover for MPT; MD analyses by VMD and XMGRACE.
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Grants
- 100256733-VIEP2024 Vicerrectoría de Investigación y Estudios de Posgrado (VIEP-BUAP, Mexico)
- 100256733-VIEP2024 Vicerrectoría de Investigación y Estudios de Posgrado (VIEP-BUAP, Mexico)
- 100256733-VIEP2024 Vicerrectoría de Investigación y Estudios de Posgrado (VIEP-BUAP, Mexico)
- 100256733-VIEP2024 Vicerrectoría de Investigación y Estudios de Posgrado (VIEP-BUAP, Mexico)
- 100256733-VIEP2024 Vicerrectoría de Investigación y Estudios de Posgrado (VIEP-BUAP, Mexico)
- BUAP-CA-263 PRODEP Academic Group (SEP, Mexico)
- BUAP-CA-263 PRODEP Academic Group (SEP, Mexico)
- BUAP-CA-263 PRODEP Academic Group (SEP, Mexico)
- BUAP-CA-263 PRODEP Academic Group (SEP, Mexico)
- BUAP-CA-263 PRODEP Academic Group (SEP, Mexico)
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Affiliation(s)
| | - Fernando Villa-Díaz
- Laboratory of Basical Science, Tecnologico Nacional de Mexico, Campus Guaymas, C.P. 85480, Sonora, Mexico
| | | | - Francisco J Melendez
- Laboratory of Theoretical Chemistry, Faculty of Chemical Sciences, BUAP, C.P. 72570, Puebla, Mexico.
| | - Thomas Scior
- Laboratory of Computational Molecular Simulations, Faculty of Chemical Sciences, BUAP, C.P. 72570, Puebla, Mexico.
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2
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Torres Juárez JA, Hernández Puga AG, Sánchez Tusie AA. Differential molecular interactions between iberiotoxin and human SLO3 and SLO1 potassium channels. J Mol Model 2025; 31:155. [PMID: 40358624 DOI: 10.1007/s00894-025-06379-8] [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: 09/26/2024] [Accepted: 04/28/2025] [Indexed: 05/15/2025]
Abstract
CONTEXT SLO1and SLO3 are similar voltage-gated K + channels. However, SLO3 expression is sperm specific and plays an important role in the hyperpolarization of the sperm membrane potential that is crucial for sperm fertilization. This makes SLO3 an excellent molecular target for the development of male contraceptives, and computational methods can facilitate structural insights for this drug development. Here, we evaluated the differential molecular interactions between the human SLO3 (hSLO3) and SLO1 (hSLO1) potassium channels and iberiotoxin (IbTX), a toxin that selectively blocks SLO channels. To do this, molecular docking and dynamics were implemented on the channel-toxin complexes to help elucidate atomistic details of their interaction and binding energy. Our analysis found that IbTX has a similar binding energy to both channels but interacts in a distinct manner with them. Particularly, Trp14 and Arg25 residues of IbTX diverges in their interaction with the residues Val283 and Asn260 residues of hSLO3 and the corresponding residues Tyr359 and Ala336 of hSLO1. Knowledge of key residues in the molecular interface of IbTX blockage can help guide and hasten non-hormonal contraceptive development. Our results encourage the use of toxins as scaffolds for specific SLO3 blockers. METHODS Atomistic molecular dynamics were implemented on the channel-toxin complexes. To generate the complexes, IbTX was docked to the channels using HADDOCK. CHARMM-GUI was used to generate simulation systems. GROMACS v2023.1 was used to run the simulations for 500 ns in an NPT ensemble at 297.26 K employing the CHARMM36 force field. Binding energy was evaluated by molecular mechanics generalized born surface area (MM/GBSA) with gmxMMPBGBSA.py.
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3
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Bing RG, Buhrman GK, Ford KC, Straub CT, Laemthong T, Rose RB, Adams MWW, Kelly RM. Structural and kinetic characterization of an acetoacetyl-Coenzyme A: acetate Coenzyme A transferase from the extreme thermophile Thermosipho melanesiensis. Biochem J 2025; 482:225-240. [PMID: 39869497 DOI: 10.1042/bcj20240747] [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: 11/20/2024] [Revised: 01/22/2025] [Accepted: 01/27/2025] [Indexed: 01/29/2025]
Abstract
Family 1 Coenzyme A transferases (CtfAB) from the extremely thermophilic bacterium, Thermosipho melanesiensis, has been used for in vivo acetone production up to 70°C. This enzyme has tentatively been identified as the rate-limiting step, due to its relatively low-binding affinity for acetate. However, existing kinetic and mechanistic studies on this enzyme are insufficient to evaluate this hypothesis. Here, kinetic analysis of purified recombinant T. melanesiensis CtfAB showed that it has a ping-pong bi-bi mechanism typical of Coenzyme A (CoA) transferases with Km values for acetate and acetoacetyl-CoA of 85 mM and 135 μM, respectively. Product inhibition by acetyl-CoA was competitive with respect to acetoacetyl-CoA and non-competitive with respect to acetate. Crystal structures of wild-type and mutant T. melanesiensis CtfAB were solved in the presence of acetate and in the presence or absence of acetyl-CoA. These structures led to a proposed structural basis for the competitive and non-competitive inhibition of acetyl-CoA: acetate binds independently of acetyl-CoA in an apparent low-affinity binding pocket in CtfA that is directly adjacent to a catalytic glutamate in CtfB. Similar to other CoA transferases, acetyl-CoA is bound in an apparent high-affinity binding site in CtfB with most interactions occurring between the phospho-ADP of CoA and CtfB residues far from the acetate binding pocket. This structural-based mechanism also explains the organic acid promiscuity of CtfAB. High-affinity interactions are predominantly between the conserved phospho-ADP of CoA, and the variable organic acid binding site is a low-affinity binding site with few specific interactions.
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Affiliation(s)
- Ryan G Bing
- Department of Chemical & Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, U.S.A
| | - Greg K Buhrman
- Biomanufacturing Training & Education Center, North Carolina State University, Raleigh, NC 27695, U.S.A
| | - Kathryne C Ford
- Department of Chemical & Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, U.S.A
| | - Christopher T Straub
- Department of Chemical & Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, U.S.A
- Current address: Novonesis, 77 Perrys Chapel Road, Franklinton, NC 27525, USA
| | - Tunyaboon Laemthong
- Department of Chemical & Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, U.S.A
- Current address: Department of Chemical Engineering, Thammasat University, Pathum Thani, Thailand
| | - Robert B Rose
- Department of Molecular & Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, U.S.A
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, U.S.A
| | - Robert M Kelly
- Department of Chemical & Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, U.S.A
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4
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Minere M, Mortensen M, Dorovykh V, Warnes G, Nizetic D, Smart TG, Hannan SB. Presynaptic hyperexcitability reversed by positive allosteric modulation of a GABABR epilepsy variant. Brain 2025; 148:533-548. [PMID: 39028675 PMCID: PMC11788220 DOI: 10.1093/brain/awae232] [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: 10/27/2023] [Revised: 04/05/2024] [Accepted: 06/23/2024] [Indexed: 07/21/2024] Open
Abstract
GABABRs are key membrane proteins that continually adapt the excitability of the nervous system. These G-protein coupled receptors are activated by the brain's premier inhibitory neurotransmitter GABA. They are obligate heterodimers composed of GABA-binding GABABR1 and G-protein-coupling GABABR2 subunits. Recently, three variants (G693W, S695I, I705N) have been identified in the gene (GABBR2) encoding for GABABR2. Individuals that harbour any of these variants exhibit severe developmental epileptic encephalopathy and intellectual disability, but the underlying pathogenesis that is triggered in neurons remains unresolved. Using a range of confocal imaging, flow cytometry, structural modelling, biochemistry, live cell Ca2+ imaging of presynaptic terminals, whole-cell electrophysiology of human embryonic kidney (HEK)-293 T cells and neurons and two-electrode voltage clamping of Xenopus oocytes, we have probed the biophysical and molecular trafficking and functional profiles of G693W, S695I and I705N variants. We report that all three point mutations impair neuronal cell surface expression of GABABRs, reducing signalling efficacy. However, a negative effect evident for one variant perturbed neurotransmission by elevating presynaptic Ca2+ signalling. This is reversed by enhancing GABABR signalling via positive allosteric modulation. Our results highlight the importance of studying neuronal receptors expressed in nervous system tissue and provide new mechanistic insights into how GABABR variants can initiate neurodevelopmental disease whilst highlighting the translational suitability and therapeutic potential of allosteric modulation for correcting these deficits.
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Affiliation(s)
- Marielle Minere
- Department of Neuroscience, Physiology and Pharmacology, University College London, London WC1E 6BT, UK
| | - Martin Mortensen
- Department of Neuroscience, Physiology and Pharmacology, University College London, London WC1E 6BT, UK
| | - Valentina Dorovykh
- Department of Neuroscience, Physiology and Pharmacology, University College London, London WC1E 6BT, UK
| | - Gary Warnes
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
| | - Dean Nizetic
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
| | - Trevor G Smart
- Department of Neuroscience, Physiology and Pharmacology, University College London, London WC1E 6BT, UK
| | - Saad B Hannan
- Department of Neuroscience, Physiology and Pharmacology, University College London, London WC1E 6BT, UK
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
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5
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Niu Y, Qin P, Lin P. Advances of deep Neural Networks (DNNs) in the development of peptide drugs. Future Med Chem 2025; 17:485-499. [PMID: 39935356 PMCID: PMC11834456 DOI: 10.1080/17568919.2025.2463319] [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: 11/24/2024] [Accepted: 01/27/2025] [Indexed: 02/13/2025] Open
Abstract
Peptides are able to bind to difficult disease targets with high potency and specificity, providing great opportunities to meet unmet medical requirements. Nevertheless, the unique features of peptides, such as their small size, high structural flexibility, and scarce data availability, bring extra challenges to the design process. Firstly, this review sums up the application of peptide drugs in treating diseases. Then, the review probes into the advantages of Deep Neural Networks (DNNs) in predicting and designing peptide structures. DNNs have demonstrated remarkable capabilities in structural prediction, enabling accurate three-dimensional modeling of peptide drugs through models like AlphaFold and its successors. Finally, the review deliberates on the challenges and coping strategies of DNNs in the development of peptide drugs, along with future research directions. Future research directions focus on further improving the accuracy and efficiency of DNN-based peptide drug design, exploring novel applications of peptide drugs, and accelerating their clinical translation. With continuous advancements in technology and data accumulation, DNNs are poised to play an increasingly crucial role in the field of peptide drug development.
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Affiliation(s)
- Yuzhen Niu
- College of Chemical Engineering and Environment, Weifang University of Science and Technology, Weifang, China
| | - Pingyang Qin
- College of Chemical Engineering and Environment, Weifang University of Science and Technology, Weifang, China
| | - Ping Lin
- College of Chemical Engineering and Environment, Weifang University of Science and Technology, Weifang, China
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6
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Wicaksono IA, Destiarani W, Romadhon SF, Nugraha BAP, Yusuf M, Milanda T, Amalia R. Transmembrane Prostate Androgen-Induced Protein 1 Molecular Modeling and Refinement Using Coarse-Grained Molecular Dynamics. ACS OMEGA 2025; 10:2712-2724. [PMID: 39895701 PMCID: PMC11780462 DOI: 10.1021/acsomega.4c08451] [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: 09/14/2024] [Revised: 12/20/2024] [Accepted: 12/26/2024] [Indexed: 02/04/2025]
Abstract
Transmembrane prostate androgen-induced protein 1 (TMEPAI), a type 1b transmembrane protein, is highly expressed in many types of cancer and is involved in cancer signaling pathways. TMEPAI affects the TGF-β, androgen receptor, Wnt, and MAPK/ERK signaling pathways. Although TMEPAI interactions are known, information about their structure is limited. This study performed TMEPAI structure prediction via a computational approach with template-free modeling using multiple Web server and refining with coarse-grained molecular dynamics to improve the understanding of its characterization, mechanism, and interactions, followed by intensive server-based validation. As a result, the predicted TMEPAI isoform structure was validated for all parameters, and the trRosetta server provided the most reliable predicted structure. This research is expected to provide preliminary scientific information about the TMEPAI structure prediction and apply it to develop targeted cancer therapy drugs.
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Affiliation(s)
- Imam Adi Wicaksono
- Department
of Pharmacology and Clinical Pharmacy, Faculty of Pharmacy, Universitas Padjadjaran, Bandung 45363, Indonesia
- Laboratory
of Translational Pharmaceutical Research, Faculty of Pharmacy, Universitas Padjadjaran, Bandung 45363, Indonesia
| | - Wanda Destiarani
- Department
of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Bandung 45363, Indonesia
| | - Shidqi Fajri Romadhon
- Department
of Pharmacology and Clinical Pharmacy, Faculty of Pharmacy, Universitas Padjadjaran, Bandung 45363, Indonesia
- Laboratory
of Translational Pharmaceutical Research, Faculty of Pharmacy, Universitas Padjadjaran, Bandung 45363, Indonesia
| | - Bagas Adi Prasetya Nugraha
- Department
of Pharmacology and Clinical Pharmacy, Faculty of Pharmacy, Universitas Padjadjaran, Bandung 45363, Indonesia
- Laboratory
of Translational Pharmaceutical Research, Faculty of Pharmacy, Universitas Padjadjaran, Bandung 45363, Indonesia
| | - Muhammad Yusuf
- Department
of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Bandung 45363, Indonesia
- Research
Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung 45363, Indonesia
| | - Tiana Milanda
- Department
of Biology Pharmacy, Faculty of Pharmacy, Universitas Padjadjaran, Bandung 45363, Indonesia
| | - Riezki Amalia
- Department
of Pharmacology and Clinical Pharmacy, Faculty of Pharmacy, Universitas Padjadjaran, Bandung 45363, Indonesia
- Laboratory
of Translational Pharmaceutical Research, Faculty of Pharmacy, Universitas Padjadjaran, Bandung 45363, Indonesia
- Center
of
Excellence in Pharmaceutical Care Innovation, Universitas Padjadjaran, Bandung 45363, Indonesia
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7
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Yegnaswamy S, C SK, Aldaais E. Conformational dynamics of the membrane protein of MERS-CoV in comparison with SARS-CoV-2 in ERGIC complex. J Biomol Struct Dyn 2025:1-15. [PMID: 39755960 DOI: 10.1080/07391102.2024.2437529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 05/21/2024] [Indexed: 01/07/2025]
Abstract
The present study explores the conformational dynamics of the membrane protein of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) within the Endoplasmic Reticulum-Golgi Intermediate Compartment (ERGIC) complex using an all-atomistic molecular dynamics simulation approach. Significant structural changes were observed in the N-terminal, C-terminal, transmembrane, and beta-sheet sandwich domains of the MERS-CoV membrane protein. This study also highlights the structural similarities between the MERS-CoV and the SARS-CoV-2 membrane proteins, particularly in how both exhibit a distinct kink in the transmembrane helix caused by aromatic residue-lipid interactions. A structural expansion below the transmembrane and above the beta-sheet sandwich domain within the dimer was observed in all the M-proteins. This site on the beta-sheet sandwich domains near the C-terminal end could serve as a potential drug-binding site. Notably, a stable helical structure was identified in the C-terminal domain of the MERS-CoV membrane protein, whereas a proper secondary structural conformation was not observed in the SARS-CoV-2 membrane protein. Further, the SARS-CoV-2 membrane protein exhibited stronger binding to the lipid bilayer than the MERS-CoV, indicating its greater structural stability within the ERGIC complex. The structural similarity between the membrane protein of MERS-CoV and SARS-CoV-2 suggests the feasibility of employing a common inhibitor against these beta-coronaviruses. Furthermore, this analysis enhances our understanding of the membrane protein's interactions with proteins and lipids, paving the way for therapeutic developments against these viruses.
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Affiliation(s)
- Subha Yegnaswamy
- School of Biotechnology and Bioinformatics, D.Y. Patil Deemed to be University, Navi Mumbai, Maharashtra, India
| | - Selvaa Kumar C
- School of Biotechnology and Bioinformatics, D.Y. Patil Deemed to be University, Navi Mumbai, Maharashtra, India
| | - Ebtisam Aldaais
- College of Applied Medical Sciences, lmam Abdulrahman Bin Faisal University (lAU), Dammam, Saudi Arabia
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8
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de La Bourdonnaye G, Ghazalova T, Fojtik P, Kutalkova K, Bednar D, Damborsky J, Rotrekl V, Stepankova V, Chaloupkova R. Computer-aided engineering of stabilized fibroblast growth factor 21. Comput Struct Biotechnol J 2024; 23:942-951. [PMID: 38379823 PMCID: PMC10877085 DOI: 10.1016/j.csbj.2024.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 02/03/2024] [Accepted: 02/03/2024] [Indexed: 02/22/2024] Open
Abstract
FGF21 is an endocrine signaling protein belonging to the family of fibroblast growth factors (FGFs). It has emerged as a molecule of interest for treating various metabolic diseases due to its role in regulating glucogenesis and ketogenesis in the liver. However, FGF21 is prone to heat, proteolytic, and acid-mediated degradation, and its low molecular weight makes it susceptible to kidney clearance, significantly reducing its therapeutic potential. Protein engineering studies addressing these challenges have generally shown that increasing the thermostability of FGF21 led to improved pharmacokinetics. Here, we describe the computer-aided design and experimental characterization of FGF21 variants with enhanced melting temperature up to 15 °C, uncompromised efficacy at activation of MAPK/ERK signaling in Hep G2 cell culture, and ability to stimulate proliferation of Hep G2 and NIH 3T3 fibroblasts cells comparable with FGF21-WT. We propose that stabilizing the FGF21 molecule by rational design should be combined with other reported stabilization strategies to maximize the pharmaceutical potential of FGF21.
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Affiliation(s)
- Gabin de La Bourdonnaye
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
- Enantis Ltd., Biotechnology Incubator INBIT, Brno, Czech Republic
| | - Tereza Ghazalova
- Enantis Ltd., Biotechnology Incubator INBIT, Brno, Czech Republic
| | - Petr Fojtik
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | | | - David Bednar
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
- Loschmidt Laboratories, Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
| | - Jiri Damborsky
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
- Loschmidt Laboratories, Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
| | - Vladimir Rotrekl
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
| | | | - Radka Chaloupkova
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
- Enantis Ltd., Biotechnology Incubator INBIT, Brno, Czech Republic
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9
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Labossiere EH, Gonzalez-Diaz S, Enns S, Lopez P, Yang X, Kidane B, Vazquez-Grande G, Siddik AB, Kung SKP, Sandstrom P, Ravandi A, Ball TB, Su RC. Detectability of cytokine and chemokine using ELISA, following sample-inactivation using Triton X-100 or heat. Sci Rep 2024; 14:26777. [PMID: 39500912 PMCID: PMC11538312 DOI: 10.1038/s41598-024-74739-0] [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: 05/02/2024] [Accepted: 09/30/2024] [Indexed: 11/08/2024] Open
Abstract
Clinical samples are routinely inactivated before molecular assays to prevent pathogen transmission. Antibody-based assays are sensitive to changes in analyte conformation, but the impact of inactivation on the analyte detectability has been overlooked. This study assessed the effects of commonly used inactivation-methods, Triton X-100 (0.5%) and heat (60 °C, 1 h), on cytokine/chemokine detection in plasma, lung aspirates, and nasopharyngeal samples. Heat significantly reduced analyte detectability in plasma (IL-12p40, IL-15, IL-16, VEGF, IL-7, TNF-β) by 33-99% (p ≤ 0.02), while Triton X-100 minimally affected analytes in plasma and nasopharyngeal samples (11-37%, p ≤ 0.04) and had no significant impact on lung aspirates. Structural analysis revealed that cytokines affected by heat had more hydrophobic residues and higher instability-indices. As the protein-detectability was affected differently in different sample types, the sample environment could also influence protein stability. This underscores the importance of selecting the most suitable inactivation methods for clinical samples to ensure accurate cytokine/chemokine analysis in both clinical and research settings.
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Affiliation(s)
- Erica Hofer Labossiere
- JC WILT Infectious Disease Research Center, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Sandra Gonzalez-Diaz
- JC WILT Infectious Disease Research Center, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, MB, Canada
- Department of Medical Microbiology & Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Stephanie Enns
- Section of Thoracic Surgery, Department of Surgery, Health Sciences Centre, University of Manitoba, Winnipeg, MB, Canada
| | - Paul Lopez
- JC WILT Infectious Disease Research Center, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Xuefen Yang
- JC WILT Infectious Disease Research Center, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Biniam Kidane
- Section of Thoracic Surgery, Department of Surgery, Health Sciences Centre, University of Manitoba, Winnipeg, MB, Canada
- Department of Physiology and Pathophysiology, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB, Canada
- Department of Biomedical Engineering, Price Faculty of Engineering, University of Manitoba, Winnipeg, MB, Canada
| | - Gloria Vazquez-Grande
- Section of Critical Care, Department of Medicine, University of Manitoba, Winnipeg, MB, Canada
| | - Abu Bakar Siddik
- JC WILT Infectious Disease Research Center, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, MB, Canada
- Department of Medical Microbiology & Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Sam Kam-Pun Kung
- Department of Immunology, University of Manitoba, Winnipeg, MB, Canada
| | - Paul Sandstrom
- JC WILT Infectious Disease Research Center, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, MB, Canada
- Department of Medical Microbiology & Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Amir Ravandi
- Cardiovascular Lipidomics, Institute of Cardiovascular Sciences, St. Boniface Hospital, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB, Canada
| | - T Blake Ball
- JC WILT Infectious Disease Research Center, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, MB, Canada
- Department of Medical Microbiology & Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Ruey-Chyi Su
- JC WILT Infectious Disease Research Center, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, MB, Canada.
- Department of Medical Microbiology & Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada.
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10
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Gallino SL, Agüero L, Boffi JC, Schottlender G, Buonfiglio P, Dalamon V, Marcovich I, Carpaneto A, Craig PO, Plazas PV, Elgoyhen AB. Key role of the TM2-TM3 loop in calcium potentiation of the α9α10 nicotinic acetylcholine receptor. Cell Mol Life Sci 2024; 81:337. [PMID: 39120784 PMCID: PMC11335262 DOI: 10.1007/s00018-024-05381-2] [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: 01/19/2024] [Revised: 07/09/2024] [Accepted: 07/23/2024] [Indexed: 08/10/2024]
Abstract
The α9α10 nicotinic cholinergic receptor (nAChR) is a ligand-gated pentameric cation-permeable ion channel that mediates synaptic transmission between descending efferent neurons and mechanosensory inner ear hair cells. When expressed in heterologous systems, α9 and α10 subunits can assemble into functional homomeric α9 and heteromeric α9α10 receptors. One of the differential properties between these nAChRs is the modulation of their ACh-evoked responses by extracellular calcium (Ca2+). While α9 nAChRs responses are blocked by Ca2+, ACh-evoked currents through α9α10 nAChRs are potentiated by Ca2+ in the micromolar range and blocked at millimolar concentrations. Using chimeric and mutant subunits, together with electrophysiological recordings under two-electrode voltage-clamp, we show that the TM2-TM3 loop of the rat α10 subunit contains key structural determinants responsible for the potentiation of the α9α10 nAChR by extracellular Ca2+. Moreover, molecular dynamics simulations reveal that the TM2-TM3 loop of α10 does not contribute to the Ca2+ potentiation phenotype through the formation of novel Ca2+ binding sites not present in the α9 receptor. These results suggest that the TM2-TM3 loop of α10 might act as a control element that facilitates the intramolecular rearrangements that follow ACh-evoked α9α10 nAChRs gating in response to local and transient changes of extracellular Ca2+ concentration. This finding might pave the way for the future rational design of drugs that target α9α10 nAChRs as otoprotectants.
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Affiliation(s)
- Sofia L Gallino
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular ''Dr. Héctor N. Torres'' (INGEBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Lucía Agüero
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular ''Dr. Héctor N. Torres'' (INGEBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Juan C Boffi
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular ''Dr. Héctor N. Torres'' (INGEBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory, Monterotondo, Italy
| | - Gustavo Schottlender
- Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Paula Buonfiglio
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular ''Dr. Héctor N. Torres'' (INGEBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Viviana Dalamon
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular ''Dr. Héctor N. Torres'' (INGEBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Irina Marcovich
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular ''Dr. Héctor N. Torres'' (INGEBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Regeneron Pharmaceuticals, Inc. Tarrytown, 10591, NY, USA
| | - Agustín Carpaneto
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular ''Dr. Héctor N. Torres'' (INGEBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Patricio O Craig
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.
- Instituto de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (IQUIBICEN), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
| | - Paola V Plazas
- Instituto de Farmacología, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
| | - Ana B Elgoyhen
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular ''Dr. Héctor N. Torres'' (INGEBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
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11
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Waterhouse AM, Studer G, Robin X, Bienert S, Tauriello G, Schwede T. The structure assessment web server: for proteins, complexes and more. Nucleic Acids Res 2024; 52:W318-W323. [PMID: 38634802 PMCID: PMC11223858 DOI: 10.1093/nar/gkae270] [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: 02/02/2024] [Revised: 03/21/2024] [Accepted: 04/02/2024] [Indexed: 04/19/2024] Open
Abstract
The 'structure assessment' web server is a one-stop shop for interactive evaluation and benchmarking of structural models of macromolecular complexes including proteins and nucleic acids. A user-friendly web dashboard links sequence with structure information and results from a variety of state-of-the-art tools, which facilitates the visual exploration and evaluation of structure models. The dashboard integrates stereochemistry information, secondary structure information, global and local model quality assessment of the tertiary structure of comparative protein models, as well as prediction of membrane location. In addition, a benchmarking mode is available where a model can be compared to a reference structure, providing easy access to scores that have been used in recent CASP experiments and CAMEO. The structure assessment web server is available at https://swissmodel.expasy.org/assess.
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Affiliation(s)
- Andrew M Waterhouse
- Biozentrum, University of Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Computational Structural Biology, Basel, Switzerland
| | - Gabriel Studer
- Biozentrum, University of Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Computational Structural Biology, Basel, Switzerland
| | - Xavier Robin
- Biozentrum, University of Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Computational Structural Biology, Basel, Switzerland
| | - Stefan Bienert
- Biozentrum, University of Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Computational Structural Biology, Basel, Switzerland
| | - Gerardo Tauriello
- Biozentrum, University of Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Computational Structural Biology, Basel, Switzerland
| | - Torsten Schwede
- Biozentrum, University of Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Computational Structural Biology, Basel, Switzerland
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12
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Rao P, Ninama J, Dudhat M, Goswami D, Rawal RM. Curcumin interferes with chitin synthesis in Aedes aegypti: a computational and experimental investigation. Mol Divers 2024; 28:1505-1529. [PMID: 37358753 DOI: 10.1007/s11030-023-10672-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 06/10/2023] [Indexed: 06/27/2023]
Abstract
Throughout history, vector-borne diseases have consistently posed significant challenges to human health. Among the strategies for vector control, chemical insecticides have seen widespread use since their inception. Nevertheless, their effectiveness is continually undermined by the steady growth of insecticide resistance within these vector populations. As such, the demand for more robust, efficient, and cost-effective natural insecticides has become increasingly pressing. One promising avenue of research focuses on chitin, a crucial structural component of mosquitoes' exoskeletons and other insects. Chitin not only provides protection and rigidity but also lends flexibility to the insect body. It undergoes substantial transformations during insect molting, a process known as ecdysis. Crucially, the production of chitin is facilitated by an enzyme known as chitin synthase, making it an attractive target for potential novel insecticides. Our recent study delved into the impacts of curcumin, a natural derivative of turmeric, on chitin synthesis and larval development in Aedes aegypti, a mosquito species known to transmit dengue and yellow fever. Our findings demonstrate that even sub-lethal amounts of curcumin can significantly reduce overall chitin content and disrupt the cuticle development in the 4th instar larvae of Aedes aegypti. Further to this, we utilized computational analyses to investigate how curcumin interacts with chitin synthase. Techniques such as molecular docking, pharmacophore feature mapping, and molecular dynamics (MD) simulations helped to illustrate that curcumin binds to the same site as polyoxin D, a recognized inhibitor of chitin synthase. These findings point to curcumin's potential as a natural, bioactive larvicide that targets chitin synthase in mosquitoes and potentially other insects.
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Affiliation(s)
- Priyashi Rao
- Department of Biochemistry & Forensic Science, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Jinal Ninama
- Department of Biochemistry & Forensic Science, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Mansi Dudhat
- Department of Biochemistry & Forensic Science, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Dweipayan Goswami
- Department of Microbiology & Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Rakesh M Rawal
- Department of Biochemistry & Forensic Science, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India.
- Department of Life Science, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India.
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13
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Ma B, Shi S, Guo W, Zhang H, Zhao Z, An H. Liensinine, a Novel and Food-Derived Compound, Exerts Potent Antihepatoma Efficacy via Inhibiting the Kv10.1 Channel. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:4689-4702. [PMID: 38382537 DOI: 10.1021/acs.jafc.3c06142] [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: 02/23/2024]
Abstract
Plant metabolites from natural product extracts offer unique advantages against carcinogenesis in the development of drugs. The target-based virtual screening from food-derived compounds represents a promising approach for tumor therapy. In this study, we performed virtual screening to target the presumed inhibitor-binding pocket and identified a highly potent Kv10.1 inhibitor, liensinine (Lien), which can inhibit the channel in a dose-dependent way with an IC50 of 0.24 ± 0.07 μM. Combining molecular dynamics simulations with mutagenesis experiments, our data show that Lien interacts with Kv10.1 by binding with Y539, T543, D551, E553, and H601 in the C-linker domain of Kv10.1. In addition, the interaction of sequence alignment and 3D structural modeling revealed differences between the C-linker domain of the Kv10.1 channel and the Kv11.1 channel. Furthermore, antitumor experiments revealed that Lien suppresses the proliferation and migration of HCC both in vitro and in vivo. In summary, the food-derived compound, Lien, may serve as a lead compound for antihepatoma therapeutic drugs targeting Kv10.1.
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Affiliation(s)
- Biao Ma
- State Key Laboratory of Reliability and Intelligence of Electrical Equipment, Hebei University of Technology, Tianjin 300401, China
- Key Laboratory of Electromagnetic Field and Electrical Apparatus Reliability of Hebei Province, Hebei University of Technology, Tianjin 300401, China
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Sciences & Biomedical Engineering, Hebei University of Technology, Tianjin 300401, China
| | - Sai Shi
- Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Wei Guo
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Sciences & Biomedical Engineering, Hebei University of Technology, Tianjin 300401, China
| | - Hailin Zhang
- Department of Pharmacology, Hebei Medical University, Shijiazhuang 050017, China
| | - Zhen Zhao
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Sciences & Biomedical Engineering, Hebei University of Technology, Tianjin 300401, China
| | - Hailong An
- State Key Laboratory of Reliability and Intelligence of Electrical Equipment, Hebei University of Technology, Tianjin 300401, China
- Key Laboratory of Electromagnetic Field and Electrical Apparatus Reliability of Hebei Province, Hebei University of Technology, Tianjin 300401, China
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Sciences & Biomedical Engineering, Hebei University of Technology, Tianjin 300401, China
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14
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Nogueira KMV, Mendes V, Kamath KS, Cheruku A, Oshiquiri LH, de Paula RG, Carraro C, Pedersoli WR, Pereira LMS, Vieira LC, Steindorff AS, Amirkhani A, McKay MJ, Nevalainen H, Molloy MP, Silva RN. Proteome profiling of enriched membrane-associated proteins unraveled a novel sophorose and cello-oligosaccharide transporter in Trichoderma reesei. Microb Cell Fact 2024; 23:22. [PMID: 38229067 DOI: 10.1186/s12934-023-02279-9] [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: 07/25/2023] [Accepted: 12/18/2023] [Indexed: 01/18/2024] Open
Abstract
BACKGROUND Trichoderma reesei is an organism extensively used in the bioethanol industry, owing to its capability to produce enzymes capable of breaking down holocellulose into simple sugars. The uptake of carbohydrates generated from cellulose breakdown is crucial to induce the signaling cascade that triggers cellulase production. However, the sugar transporters involved in this process in T. reesei remain poorly identified and characterized. RESULTS To address this gap, this study used temporal membrane proteomics analysis to identify five known and nine putative sugar transporters that may be involved in cellulose degradation by T. reesei. Docking analysis pointed out potential ligands for the putative sugar transporter Tr44175. Further functional validation of this transporter was carried out in Saccharomyces cerevisiae. The results showed that Tr44175 transports a variety of sugar molecules, including cellobiose, cellotriose, cellotetraose, and sophorose. CONCLUSION This study has unveiled a transporter Tr44175 capable of transporting cellobiose, cellotriose, cellotetraose, and sophorose. Our study represents the first inventory of T. reesei sugar transportome once exposed to cellulose, offering promising potential targets for strain engineering in the context of bioethanol production.
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Affiliation(s)
- Karoline Maria Vieira Nogueira
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirao Preto Medical School (FMRP), University of Sao Paulo, Ribeirao Preto, SP, Brazil
| | - Vanessa Mendes
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirao Preto Medical School (FMRP), University of Sao Paulo, Ribeirao Preto, SP, Brazil
| | - Karthik Shantharam Kamath
- Department of Natural Sciences, Macquarie University, Sydney, NSW, Australia
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW, Australia
| | - Anusha Cheruku
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW, Australia
| | - Letícia Harumi Oshiquiri
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirao Preto Medical School (FMRP), University of Sao Paulo, Ribeirao Preto, SP, Brazil
| | - Renato Graciano de Paula
- Department of Physiological Sciences, Health Sciences Centre, Federal University of Espirito Santo, Vitoria, ES, 29047-105, Brazil
| | - Claudia Carraro
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirao Preto Medical School (FMRP), University of Sao Paulo, Ribeirao Preto, SP, Brazil
| | - Wellington Ramos Pedersoli
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirao Preto Medical School (FMRP), University of Sao Paulo, Ribeirao Preto, SP, Brazil
| | - Lucas Matheus Soares Pereira
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirao Preto Medical School (FMRP), University of Sao Paulo, Ribeirao Preto, SP, Brazil
| | - Luiz Carlos Vieira
- Department of Molecular and Cell Biology, Ribeirao Preto Medical School (FMRP), University of Sao Paulo, Ribeirao Preto, SP, Brazil
| | - Andrei Stecca Steindorff
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ardeshir Amirkhani
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW, Australia
| | - Matthew J McKay
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW, Australia
| | - Helena Nevalainen
- Department of Natural Sciences, Macquarie University, Sydney, NSW, Australia
| | - Mark P Molloy
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW, Australia
| | - Roberto N Silva
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirao Preto Medical School (FMRP), University of Sao Paulo, Ribeirao Preto, SP, Brazil.
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15
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Ma B, Shi S, Ren S, Qu C, Zhao Z, An H. Corydaline binds to a druggable pocket of hEAG1 channel and inhibits hepatic carcinoma cell viability. Eur J Pharmacol 2024; 962:176240. [PMID: 38048981 DOI: 10.1016/j.ejphar.2023.176240] [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: 08/11/2023] [Revised: 11/22/2023] [Accepted: 11/28/2023] [Indexed: 12/06/2023]
Abstract
Ether-à-go-go (EAG) potassium channels play a crucial role in the regulation of neuronal excitability and cancer progression, rendering them potential drug targets for cancer therapy. However, the scarcity of information regarding the selection sites on hEAG1 has posed a challenge in the discovery of new hEAG1 inhibitors. In this study, we introduced a novel natural product, corydaline, which selectively inhibits the hEAG1 channel without sensitivity to other KCNH channels. The IC50 of corydaline for the hEAG1 channel was 11.3 ± 0.6 μM, whereas the IC50 for hEAG2 and hERG1 were 73.6 ± 9.9 μM and 111.4 ± 8.5 μM, respectively. Molecular dynamics simulations together with site-directed mutagenesis, have unveiled that the site corydaline forms interactions with Lys217, Phe273, Pro276, Trp295 and Arg366, situated within the intracellular transmembrane segments S1-S4 of the voltage-sensor domain, be considered a novel drug pocket for hEAG1. Additionally, the intergaration of sequence alignment and 3D structural modeling revealed differences between the voltage sensor domain of hEAG1 channel and other EAG channels, suggesting the feasibility of a VSD modulation approach that could potentially lead to the selective inhibition of hEAG1 channels. Furthermore, antitumor experiments demonstrated that corydaline can inhibit the proliferation and migration of hepatic carcinoma cells by targeting hEAG1. The identification of this novel druggable pocket offers the possibility for drug screening against diseases linked to abnormal hEAG1 channels.
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Affiliation(s)
- Biao Ma
- State Key Laboratory of Reliability and Intelligence of Electrical Equipment, Hebei University of Technology, Tianjin, 300401, China; Key Laboratory of Electromagnetic Field and Electrical Apparatus Reliability of Hebei Province, Hebei University of Technology, Tianjin, 300401, China; Key Laboratory of Molecular Biophysics, Hebei Province, China; Institute of Biophysics, School of Health Sciences and Biomedical Engineering, Hebei University of Technology, Tianjin, 300401, China
| | - Sai Shi
- Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, 300072, China
| | - Shuxi Ren
- School of Sciences, Hebei University of Technology, Tianjin, 300401, China
| | - Chang Qu
- State Key Laboratory of Reliability and Intelligence of Electrical Equipment, Hebei University of Technology, Tianjin, 300401, China; Key Laboratory of Electromagnetic Field and Electrical Apparatus Reliability of Hebei Province, Hebei University of Technology, Tianjin, 300401, China; Key Laboratory of Molecular Biophysics, Hebei Province, China; Institute of Biophysics, School of Health Sciences and Biomedical Engineering, Hebei University of Technology, Tianjin, 300401, China
| | - Zhen Zhao
- Key Laboratory of Molecular Biophysics, Hebei Province, China; Institute of Biophysics, School of Health Sciences and Biomedical Engineering, Hebei University of Technology, Tianjin, 300401, China.
| | - Hailong An
- State Key Laboratory of Reliability and Intelligence of Electrical Equipment, Hebei University of Technology, Tianjin, 300401, China; Key Laboratory of Electromagnetic Field and Electrical Apparatus Reliability of Hebei Province, Hebei University of Technology, Tianjin, 300401, China; Key Laboratory of Molecular Biophysics, Hebei Province, China; Institute of Biophysics, School of Health Sciences and Biomedical Engineering, Hebei University of Technology, Tianjin, 300401, China.
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16
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Biswas S, Hossen MR, Akter S, Ali MA, Halim MA, Ullah MO. Structural dynamics and functional analysis of Saprolegnia parasitica chitin synthases 5 in a phospholipid bilayer. J Biomol Struct Dyn 2024; 42:461-474. [PMID: 36995127 DOI: 10.1080/07391102.2023.2193993] [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: 08/13/2022] [Accepted: 03/15/2023] [Indexed: 03/31/2023]
Abstract
Saprolegnia parasitica is an oomycete responsible for a fish disease called saprolegniosis, which poses an economic and environmental burden on aquaculture production. In Saprolegnia, CHS5 of S. parasitica (SpCHS5) contains an N-terminal domain, a catalytic domain of the glycosyltransferase -2 family containing a GT-A fold, and a C-terminal transmembrane domain. No three-dimensional structure of SpCHS5 is reported yet disclosing the structural details of this protein. We have developed a structural model of full-length SpCHS5 and validated it by molecular dynamics simulation technique. From the 1 microsecond simulations, we retrieved the stable RoseTTAFold model SpCHS5 protein to explain characteristics and structural features. Furthermore, from the analysis of the movement of chitin in the protein cavity, we assumed that ARG 482, GLN 527, PHE 529, PHE 530, LEU 540, SER 541, TYR 544, ASN 634, THR 641, TYR 645, THR 641, ASN 772 residues as a main cavity lining site. In SMD analysis, we investigated the opening of the transmembrane cavity required for chitin translocation. The pulling of chitin from the internal cavity to the extracellular region was observed through steered molecular dynamics simulations. A comparison of the initial and final structures of chitin complex showed that there's a transmembrane cavity opening in the simulations. Overall, this present work will help us understand the structural and functional basis of CHS5 and design inhibitors against SpCHS5.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sourav Biswas
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
- Department of Chemistry, Clemson University, Clemson, SC, USA
| | - Md Rubel Hossen
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Shaila Akter
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Md Ackas Ali
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, USA
| | - Mohammad A Halim
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, USA
| | - M Obayed Ullah
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
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17
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Bains A, Fischer K, Guan W, LiWang PJ. The Antiviral Activity of the Lectin Griffithsin against SARS-CoV-2 Is Enhanced by the Presence of Structural Proteins. Viruses 2023; 15:2452. [PMID: 38140693 PMCID: PMC10747160 DOI: 10.3390/v15122452] [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: 10/14/2023] [Revised: 12/07/2023] [Accepted: 12/14/2023] [Indexed: 12/24/2023] Open
Abstract
Although COVID-19 transmission has been reduced by the advent of vaccinations and a variety of rapid monitoring techniques, the SARS-CoV-2 virus itself has shown a remarkable ability to mutate and persist. With this long track record of immune escape, researchers are still exploring prophylactic treatments to curtail future SARS-CoV-2 variants. Specifically, much focus has been placed on the antiviral lectin Griffithsin in preventing spike protein-mediated infection via the hACE2 receptor (direct infection). However, an oft-overlooked aspect of SARS-CoV-2 infection is viral capture by attachment receptors such as DC-SIGN, which is thought to facilitate the initial stages of COVID-19 infection in the lung tissue (called trans-infection). In addition, while immune escape is dictated by mutations in the spike protein, coronaviral virions also incorporate M, N, and E structural proteins within the particle. In this paper, we explored how several structural facets of both the SARS-CoV-2 virion and the antiviral lectin Griffithsin can affect and attenuate the infectivity of SARS-CoV-2 pseudovirus. We found that Griffithsin was a better inhibitor of hACE2-mediated direct infection when the coronaviral M protein is present compared to when it is absent (possibly providing an explanation regarding why Griffithsin shows better inhibition against authentic SARS-CoV-2 as opposed to pseudotyped viruses, which generally do not contain M) and that Griffithsin was not an effective inhibitor of DC-SIGN-mediated trans-infection. Furthermore, we found that DC-SIGN appeared to mediate trans-infection exclusively via binding to the SARS-CoV-2 spike protein, with no significant effect observed when other viral proteins (M, N, and/or E) were present. These results provide etiological data that may help to direct the development of novel antiviral treatments, either by leveraging Griffithsin binding to the M protein as a novel strategy to prevent SARS-CoV-2 infection or by narrowing efforts to inhibit trans-infection to focus on DC-SIGN binding to SARS-CoV-2 spike protein.
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Affiliation(s)
- Arjan Bains
- Chemistry and Biochemistry, University of California Merced, 5200 North Lake Rd., Merced, CA 95343, USA;
| | - Kathryn Fischer
- Quantitative and Systems Biology, University of California Merced, 5200 North Lake Rd., Merced, CA 95343, USA;
| | - Wenyan Guan
- Materials and Biomaterials Science and Engineering, University of California Merced, 5200 North Lake Rd., Merced, CA 95343, USA;
| | - Patricia J. LiWang
- Molecular Cell Biology, Health Sciences Research Institute, University of California Merced, 5200 North Lake Rd., Merced, CA 95343, USA
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18
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Zhao Y, Zheng Z, Zhang Z, Xu Y, Hillpot E, Lin YS, Zakusilo FT, Lu JY, Ablaeva J, Biashad SA, Miller RA, Nevo E, Seluanov A, Gorbunova V. Evolution of high-molecular-mass hyaluronic acid is associated with subterranean lifestyle. Nat Commun 2023; 14:8054. [PMID: 38052795 PMCID: PMC10698142 DOI: 10.1038/s41467-023-43623-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 11/15/2023] [Indexed: 12/07/2023] Open
Abstract
Hyaluronic acid is a major component of extracellular matrix which plays an important role in development, cellular response to injury and inflammation, cell migration, and cancer. The naked mole-rat (Heterocephalus glaber) contains abundant high-molecular-mass hyaluronic acid in its tissues, which contributes to this species' cancer resistance and possibly to its longevity. Here we report that abundant high-molecular-mass hyaluronic acid is found in a wide range of subterranean mammalian species, but not in phylogenetically related aboveground species. These subterranean mammalian species accumulate abundant high-molecular-mass hyaluronic acid by regulating the expression of genes involved in hyaluronic acid degradation and synthesis and contain unique mutations in these genes. The abundant high-molecular-mass hyaluronic acid may benefit the adaptation to subterranean environment by increasing skin elasticity and protecting from oxidative stress due to hypoxic conditions. Our work suggests that high-molecular-mass hyaluronic acid has evolved with subterranean lifestyle.
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Affiliation(s)
- Yang Zhao
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
- Department of Physiology and Department of Hepatobiliary and Pancreatic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 301158, China
| | - Zhizhong Zheng
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Zhihui Zhang
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Yandong Xu
- Department of Physiology and Department of Hepatobiliary and Pancreatic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 301158, China
| | - Eric Hillpot
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Yifei S Lin
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Frances T Zakusilo
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - J Yuyang Lu
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Julia Ablaeva
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Seyed Ali Biashad
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Richard A Miller
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, Haifa, 3498838, Israel
| | - Andrei Seluanov
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA.
- Department of Medicine, University of Rochester School of Medicine, Rochester, NY, 14627, USA.
| | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA.
- Department of Medicine, University of Rochester School of Medicine, Rochester, NY, 14627, USA.
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Zhao Y, Zheng Z, Zhang Z, Hillpot E, Lin YS, Zakusilo FT, Lu JY, Ablaeva J, Miller RA, Nevo E, Seluanov A, Gorbunova V. Evolution of High-Molecular-Mass Hyaluronic Acid is Associated with Subterranean Lifestyle. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.08.539764. [PMID: 37215017 PMCID: PMC10197608 DOI: 10.1101/2023.05.08.539764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Hyaluronic acid (HA) is a major component of extracellular matrix (ECM) which plays an important role in development, cellular response to injury and inflammation, cell migration, and cancer. The naked mole-rat (NMR, Heterocephalus glaber ) contains abundant high-molecular-mass HA (HMM-HA) in its tissues, which contributes to this species' cancer resistance and possibly longevity. Here we report that abundant HMM-HA is found in a wide range of subterranean mammalian species, but not in phylogenetically related aboveground species. These species accumulate abundant HMM-HA by regulating the expression of genes involved in HA degradation and synthesis and contain unique mutations in these genes. The abundant high molecular weight HA may benefit the adaptation to subterranean environment by increasing skin elasticity and protecting from oxidative stress due to hypoxic subterranean environment. HMM-HA may also be coopted to confer cancer resistance and longevity to subterranean mammals. Our work suggests that HMM-HA has evolved with subterranean lifestyle.
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Jamali Langeroudi A, Sabet MS, Jalali-Javaran M, Zamani K, Lohrasebi T, Malboobi MA. Functional assessment of AtPAP17; encoding a purple acid phosphatase involved in phosphate metabolism in Arabidopsis thaliana. Biotechnol Lett 2023; 45:719-739. [PMID: 37074554 DOI: 10.1007/s10529-023-03375-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 03/05/2023] [Accepted: 04/03/2023] [Indexed: 04/20/2023]
Abstract
PURPOSE Purple acid phosphatases (PAPs) includ the largest classes of non-specific plant acid phosphatases. Most characterized PAPs were found to play physiological functions in phosphorus metabolism. In this study, we investigated the function of AtPAP17 gene encoding an important purple acid phosphatase in Arabidopsis thaliana. METHODS The full-length cDNA sequence of AtPAP17 gene under the control of CaMV-35S promoter was transferred to the A. thaliana WT plant. The generated homozygote AtPAP17-overexpressed plants were compared by the types of analyses with corresponding homozygote atpap17-mutant plant and WT in both + P (1.2 mM) and - P (0 mM) conditions. RESULTS In the + P condition, the highest and the lowest amount of Pi was observed in AtPAP17-overexpressed plants and atpap17-mutant plants by 111% increase and 38% decrease compared with the WT plants, respectively. Furthermore, under the same condition, APase activity of AtPAP17-overexpressed plants increased by 24% compared to the WT. Inversely, atpap17-mutant plant represented a 71% fall compared to WT plants. The comparison of fresh weight and dry weight in the studied plants showed that the highest and the lowest amount of absorbed water belonged to OE plants (with 38 and 12 mg plant-1) and Mu plants (with 22 and 7 mg plant-1) in + P and - P conditions, respectively. CONCLUSION The lack of AtPAP17 gene in the A. thaliana genome led to a remarkable reduction in the development of root biomass. Thus, AtPAP17 could have an important role in the root but not shoot developmental and structural programming. Consequently, this function enables them to absorb more water and eventually associated with more phosphate absorption.
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Affiliation(s)
- Arash Jamali Langeroudi
- Department of Agricultural Biotechnology, Faculty of Agriculture, Tarbiat Modares University, P.O. Box 14115-336, Tehran, Iran
| | - Mohammad Sadegh Sabet
- Department of Plant Genetics and Breeding, Faculty of Agriculture, Tarbiat Modares University, P.O. Box 14115-336, Tehran, Iran.
| | - Mokhtar Jalali-Javaran
- Department of Agricultural Biotechnology, Faculty of Agriculture, Tarbiat Modares University, P.O. Box 14115-336, Tehran, Iran
| | - Katayoun Zamani
- Department of Genetic Engineering and Biosafety, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, and Extension Organization, Karaj, Tehran, Iran
| | - Tahmineh Lohrasebi
- Department of Plant Biotechnology, National Institute of Genetic Engineering and Biotechnology, P.O. Box 14965-161, Tehran, Iran
| | - Mohammad Ali Malboobi
- Department of Plant Biotechnology, National Institute of Genetic Engineering and Biotechnology, P.O. Box 14965-161, Tehran, Iran
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Yang T, Wang Y, Jiang J, Wang P, Zhong Y, Zhou Q, Wang X, Cai J, Huang M, Jiang D, Dai T, Cao W. Influence of High-Molecular-Weight Glutenin Subunit on Components and Multiscale Structure of Gluten and Dough Quality in Soft Wheat. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:4943-4956. [PMID: 36924464 DOI: 10.1021/acs.jafc.2c07958] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
A set of high-molecular-weight glutenin subunit (HMW-GS) deletion lines were used to investigate the influences of HMW-GS on wheat gluten, and dough properties were investigated using a set of HMW-GS deletion lines. Results showed that HMW-GS deletion significantly decreased the dough stability time, as well as viscoelastic moduli (G' and G″), compared with the wild type, where the deletion of x-type HMW-GSs (Ax1d, Bx7d, and Dy12d) decreased more than y-type HMW-GSs (By8d and Dy12d). The deletion of HMW-GS significantly decreased HMW-GS contents and increased α-/γ-gliadin contents. A proteomic study showed that the HMW-GS deletion down-regulated the HMW-GS, β-amylase, serpins, and protein disulfide isomerase and up-regulated the LMW-GS, α/γ-gliadin, and α-amylase inhibitor. Meanwhile, HMW-GS deletion significantly decreased contents of β-turn and β-sheet. In addition, less energetically stable disulfide conformations (trans-gauche-gauche and trans-gauche-trans) were abundant in HMW-GS deletion lines. Furthermore, analysis of five HMW-GSs based on amino acid sequences proved that Dx2 and Bx7 had a more stable structure, followed by Ax1, then Dy12, and finally By8.
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Affiliation(s)
- Tao Yang
- National Technique Innovation Center for Regional Wheat Production/Key Laboratory of Crop Physiology, Ecology and Management, Ministry of Agriculture/National Engineering and Technology Center for Information Agriculture, College of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China
| | - Yingpeng Wang
- National Technique Innovation Center for Regional Wheat Production/Key Laboratory of Crop Physiology, Ecology and Management, Ministry of Agriculture/National Engineering and Technology Center for Information Agriculture, College of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China
| | - Jiali Jiang
- National Technique Innovation Center for Regional Wheat Production/Key Laboratory of Crop Physiology, Ecology and Management, Ministry of Agriculture/National Engineering and Technology Center for Information Agriculture, College of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China
| | - Pei Wang
- National Technique Innovation Center for Regional Wheat Production/Key Laboratory of Crop Physiology, Ecology and Management, Ministry of Agriculture/National Engineering and Technology Center for Information Agriculture, College of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China
| | - Yingxin Zhong
- National Technique Innovation Center for Regional Wheat Production/Key Laboratory of Crop Physiology, Ecology and Management, Ministry of Agriculture/National Engineering and Technology Center for Information Agriculture, College of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China
| | - Qin Zhou
- National Technique Innovation Center for Regional Wheat Production/Key Laboratory of Crop Physiology, Ecology and Management, Ministry of Agriculture/National Engineering and Technology Center for Information Agriculture, College of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China
| | - Xiao Wang
- National Technique Innovation Center for Regional Wheat Production/Key Laboratory of Crop Physiology, Ecology and Management, Ministry of Agriculture/National Engineering and Technology Center for Information Agriculture, College of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China
| | - Jian Cai
- National Technique Innovation Center for Regional Wheat Production/Key Laboratory of Crop Physiology, Ecology and Management, Ministry of Agriculture/National Engineering and Technology Center for Information Agriculture, College of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China
| | - Mei Huang
- National Technique Innovation Center for Regional Wheat Production/Key Laboratory of Crop Physiology, Ecology and Management, Ministry of Agriculture/National Engineering and Technology Center for Information Agriculture, College of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China
| | - Dong Jiang
- National Technique Innovation Center for Regional Wheat Production/Key Laboratory of Crop Physiology, Ecology and Management, Ministry of Agriculture/National Engineering and Technology Center for Information Agriculture, College of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China
| | - Tingbo Dai
- National Technique Innovation Center for Regional Wheat Production/Key Laboratory of Crop Physiology, Ecology and Management, Ministry of Agriculture/National Engineering and Technology Center for Information Agriculture, College of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China
| | - Weixing Cao
- National Technique Innovation Center for Regional Wheat Production/Key Laboratory of Crop Physiology, Ecology and Management, Ministry of Agriculture/National Engineering and Technology Center for Information Agriculture, College of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China
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Leiva S, Bugnon Valdano M, Gardiol D. Unravelling the epidemiological diversity of Zika virus by analyzing key protein variations. Arch Virol 2023; 168:115. [PMID: 36943525 DOI: 10.1007/s00705-023-05726-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 01/19/2023] [Indexed: 03/23/2023]
Abstract
The consequences of Zika virus (ZIKV) infections were limited to sporadic mild diseases until almost a decade ago, when epidemic outbreaks took place, with quick spread into the Americas. Simultaneously, novel severe neurological manifestations of ZIKV infections were identified, including congenital microcephaly. However, why the epidemic strains behave differently is not yet completely understood, and many questions remain about the actual significance of genetic variations in the epidemiology and biology of ZIKV. In this study, we analysed a large number of viral sequences to identify genes with different levels of variability and patterns of genomic variations that could be associated with ZIKV diversity. We compared numerous epidemic strains with pre-epidemic strains, using the BWA-mem algorithm, and we also examined specific variations among the epidemic ZIKV strains derived from microcephaly cases. We identified several viral genes with dissimilar mutation rates among the ZIKV strain groups and novel protein variation profiles that might be associated with epidemiological particularities. Finally, we assessed the impact of the detected changes on the structure and stability of the NS1, NS5, and E proteins using the I-TASSER, trRosetta, and RaptorX modelling algorithms, and we found some interesting variations that might help to explain the heterogeneous features of the diverse ZIKA strains. This work contributes to the identification of genetic differences in the ZIKV genome that might have a phenotypic impact, providing a basis for future experimental analysis to elucidate the genetic causes of the recent ZIKV emergency.
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Affiliation(s)
- Santiago Leiva
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Biología Molecular y Celular de Rosario-CONICET, Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - Marina Bugnon Valdano
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Biología Molecular y Celular de Rosario-CONICET, Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina.
| | - Daniela Gardiol
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Biología Molecular y Celular de Rosario-CONICET, Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina.
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Jaciuk M, Scherf D, Kaszuba K, Gaik M, Rau A, Kościelniak A, Krutyhołowa R, Rawski M, Indyka P, Graziadei A, Chramiec-Głąbik A, Biela A, Dobosz D, Lin TY, Abbassi NEH, Hammermeister A, Rappsilber J, Kosinski J, Schaffrath R, Glatt S. Cryo-EM structure of the fully assembled Elongator complex. Nucleic Acids Res 2023; 51:2011-2032. [PMID: 36617428 PMCID: PMC10018365 DOI: 10.1093/nar/gkac1232] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 11/22/2022] [Accepted: 12/09/2022] [Indexed: 01/10/2023] Open
Abstract
Transfer RNA (tRNA) molecules are essential to decode messenger RNA codons during protein synthesis. All known tRNAs are heavily modified at multiple positions through post-transcriptional addition of chemical groups. Modifications in the tRNA anticodons are directly influencing ribosome decoding and dynamics during translation elongation and are crucial for maintaining proteome integrity. In eukaryotes, wobble uridines are modified by Elongator, a large and highly conserved macromolecular complex. Elongator consists of two subcomplexes, namely Elp123 containing the enzymatically active Elp3 subunit and the associated Elp456 hetero-hexamer. The structure of the fully assembled complex and the function of the Elp456 subcomplex have remained elusive. Here, we show the cryo-electron microscopy structure of yeast Elongator at an overall resolution of 4.3 Å. We validate the obtained structure by complementary mutational analyses in vitro and in vivo. In addition, we determined various structures of the murine Elongator complex, including the fully assembled mouse Elongator complex at 5.9 Å resolution. Our results confirm the structural conservation of Elongator and its intermediates among eukaryotes. Furthermore, we complement our analyses with the biochemical characterization of the assembled human Elongator. Our results provide the molecular basis for the assembly of Elongator and its tRNA modification activity in eukaryotes.
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Affiliation(s)
- Marcin Jaciuk
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
| | - David Scherf
- Institute for Biology, Department for Microbiology, University of Kassel, Kassel 34132, Germany
| | - Karol Kaszuba
- European Molecular Biology Laboratory Hamburg, Hamburg 22607, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg 22607, Germany
| | - Monika Gaik
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
| | - Alexander Rau
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin 13355, Germany
| | - Anna Kościelniak
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
| | - Rościsław Krutyhołowa
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
| | - Michał Rawski
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
- National Synchrotron Radiation Centre SOLARIS, Jagiellonian University, Krakow 30-387, Poland
| | - Paulina Indyka
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
- National Synchrotron Radiation Centre SOLARIS, Jagiellonian University, Krakow 30-387, Poland
| | - Andrea Graziadei
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin 13355, Germany
| | | | - Anna Biela
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
| | - Dominika Dobosz
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
| | - Ting-Yu Lin
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
| | - Nour-el-Hana Abbassi
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw 02-091, Poland
| | - Alexander Hammermeister
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
- Institute for Biology, Department for Microbiology, University of Kassel, Kassel 34132, Germany
| | - Juri Rappsilber
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin 13355, Germany
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Jan Kosinski
- European Molecular Biology Laboratory Hamburg, Hamburg 22607, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg 22607, Germany
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Raffael Schaffrath
- Institute for Biology, Department for Microbiology, University of Kassel, Kassel 34132, Germany
| | - Sebastian Glatt
- To whom correspondence should be addressed. Tel: +48 12 664 6321; Fax: +48 12 664 6902;
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Siddiqui AJ, Kumar V, Jahan S, Alshahrani MM, Al Awadh AA, Siddiqui MA, Hamadou WS, Abdelgadir A, Saxena J, Badraoui R, Snoussi M, Adnan M. Computational insight into structural basis of human ELOVL1 inhibition. Comput Biol Med 2023; 157:106786. [PMID: 36924735 DOI: 10.1016/j.compbiomed.2023.106786] [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: 11/09/2022] [Revised: 02/17/2023] [Accepted: 03/10/2023] [Indexed: 03/13/2023]
Abstract
Very long-chain fatty acids (VLCFAs) play a direct role in the development of a neurological disorder, X-linked adrenoleukodystrophy (X-ALD). Since ELOVL1 catalyzes the rate-limiting step of the synthesis of VLCFAs, it has emerged as an attractive target for the treatment of X-ALD. Recently two potent inhibitors, compound 22 (C22) and compound 27 (C27) have been reported to specifically inhibit human ELOVL1 but their structural basis of inhibition has not been explored. In the present study, we have used a homology model of human ELOVL1 to deduce the binding site and binding modes of C22 and C27. We have employed computational approaches to characterize the binding of C22 and C27. Initially, binding of hexacosanoyl-CoA (C26:0-CoA) to ELOVL1 was modelled and further validated by molecular dynamics (MD) simulation. We observed that the fatty acid tail of C26: CoA protrudes from a unique opening located at the occluded end of ELOVL1. Structural comparison of ELOVL1 with the crystal structure of ELOVL7 revealed that the unique opening was not present in human ELOVL7. Combined blind and focused molecular docking approaches revealed that C22 and C27 exhibit favourable binding in the same unique opening. Further, MD simulations and free binding energy calculations confirmed that C22 and C27 maintain the favourable binding in the unique opening of ELOVL1. Overall, our findings suggest that selective human ELOVL1 inhibitors block the binding of long tails of VLCFAs near the occluded end of ELOVL1. Present study will be helpful in the discovery and design of novel, selective and potent inhibitors of human ELOVL1.
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Affiliation(s)
- Arif Jamal Siddiqui
- Department of Biology, College of Science, University of Ha'il, Ha'il, P.O. Box 2440, Saudi Arabia; Molecular Diagnostics and Personalized Therapeutics Unit, University of Ha'il, Ha'il, P O Box 2440, Saudi Arabia.
| | - Vikash Kumar
- JeevikaSilicoBio, Lucknow, Uttar Pradesh, 226014, India.
| | - Sadaf Jahan
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah, 11952, Saudi Arabia.
| | - Mohammed Merae Alshahrani
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, 1988, Najran, 61441, Saudi Arabia.
| | - Ahmed Abdullah Al Awadh
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, 1988, Najran, 61441, Saudi Arabia.
| | - Maqsood Ahmed Siddiqui
- Department of Zoology, College of Science, King Saud University, P.O. Box: 2455, Riyadh, 11451, Saudi Arabia.
| | - Walid Sabri Hamadou
- Department of Biology, College of Science, University of Ha'il, Ha'il, P.O. Box 2440, Saudi Arabia; Molecular Diagnostics and Personalized Therapeutics Unit, University of Ha'il, Ha'il, P O Box 2440, Saudi Arabia.
| | - Abdelmushin Abdelgadir
- Department of Biology, College of Science, University of Ha'il, Ha'il, P.O. Box 2440, Saudi Arabia; Molecular Diagnostics and Personalized Therapeutics Unit, University of Ha'il, Ha'il, P O Box 2440, Saudi Arabia.
| | - Juhi Saxena
- Department of Biotechnology, University Institute of Biotechnology, Chandigarh University, Gharuan, NH- 95, Ludhiana - Chandigarh State Hwy, Punjab, 140413, India.
| | - Riadh Badraoui
- Department of Biology, College of Science, University of Ha'il, Ha'il, P.O. Box 2440, Saudi Arabia; Molecular Diagnostics and Personalized Therapeutics Unit, University of Ha'il, Ha'il, P O Box 2440, Saudi Arabia.
| | - Mejdi Snoussi
- Department of Biology, College of Science, University of Ha'il, Ha'il, P.O. Box 2440, Saudi Arabia; Molecular Diagnostics and Personalized Therapeutics Unit, University of Ha'il, Ha'il, P O Box 2440, Saudi Arabia.
| | - Mohd Adnan
- Department of Biology, College of Science, University of Ha'il, Ha'il, P.O. Box 2440, Saudi Arabia; Molecular Diagnostics and Personalized Therapeutics Unit, University of Ha'il, Ha'il, P O Box 2440, Saudi Arabia.
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Afshinpour M, Mahdiuni H. Arginine transportation mechanism through cationic amino acid transporter 1: insights from molecular dynamics studies. J Biomol Struct Dyn 2023; 41:13580-13594. [PMID: 36762692 DOI: 10.1080/07391102.2023.2175374] [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: 07/21/2022] [Accepted: 01/28/2023] [Indexed: 02/11/2023]
Abstract
Metabolic and signaling mechanisms in mammalian cells are facilitated by the transportation of L-arginine (Arg) across the plasma membrane through cationic amino acid transporter (CAT) proteins. Due to a lack of argininosuccinate synthase (ASS) activity in various tumor cells such as acute myeloid leukemia, acute lymphocytic leukemia, and chronic lymphocytic leukemia, these tumor entities are arginine-auxotrophic and therefore depend on the uptake of the amino acid arginine. Cationic amino acid transporter-1 (CAT-1) is the leading arginine importer expressed in the aforementioned tumor entities. Hence, in the present study, to investigate the transportation mechanism of arginine in CAT-1, we performed molecular dynamics (MD) simulation methods on the modeled human CAT-1. The MM-PBSA approach was conducted to determine the critical residues interacting with arginine within the corresponding binding site of CAT-1. In addition, we found out that the water molecules have the leading role in forming the transportation channel within CAT-1. The conductive structure of CAT-1 was formed only when the water molecules were continuously distributed across the channel. Steered molecular dynamics (SMD) simulation approach showed various energy barriers against arginine transportation through CAT-1, especially while crossing the bottlenecks of the related channel. These findings at the molecular level might shed light on identifying the crucial amino acids in the binding of arginine to eukaryotic CATs and also provide fundamental insights into the arginine transportation mechanisms through CAT-1. Understanding the transportation mechanism of arginine is essential to developing CAT-1 blockers, which can be potential medications for some types of cancers.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Maral Afshinpour
- Bioinformatics Lab., Department of Biology, School of Sciences, Razi University, Kermanshah, Iran
| | - Hamid Mahdiuni
- Bioinformatics Lab., Department of Biology, School of Sciences, Razi University, Kermanshah, Iran
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L-proline transporter inhibitor (LQFM215) promotes neuroprotection in ischemic stroke. Pharmacol Rep 2023; 75:276-292. [PMID: 36719635 DOI: 10.1007/s43440-023-00451-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 02/01/2023]
Abstract
BACKGROUND L-proline transporter (PROT/SLC6A7) is closely associated with glutamatergic neurotransmission, where L-proline modulates the NMDA receptor (NMDAR) function. NMDAR-mediated excitotoxicity is a primary cause of neuronal death following stroke, which is triggered by the uncontrolled release of glutamate during the ischemic process. After ischemic stroke, L-proline levels show a reduction in the plasma, but high circulating levels of this molecule indicate good functional recovery. This work aimed to produce new PROT inhibitors and explore their effects on ischemic stroke. METHODS Initially, we built a three-dimensional model of the PROT protein and run a molecular docking with the newly designed compounds (LQFM215, LQFM216, and LQFM217). Then, we synthesized new PROT inhibitors by molecular hybridization, and proline uptake was measured in ex vivo and in vivo models. The behavioral characterization of the treated mice was performed by the open-field test, elevated plus-maze, Y-maze, and forced swimming test. We used the permanent middle cerebral artery occlusion (MCAO) model to study the ischemic stroke damage and analyzed the motor impairment with limb clasping or cylinder tests. RESULTS LQFM215 inhibited proline uptake in hippocampal synaptosomes, and the LQFM215 treatment reduced proline levels in the mouse hippocampus. LQFM215 reduced the locomotor and exploratory activity in mice and did not show any anxiety-related or working memory impairments. In the MCAO model, LQFM215 pre-treatment and treatment reduced the infarcted area and reduced motor impairments in the cylinder test and limb clasping. CONCLUSIONS This dataset suggests that the new compounds inhibit cerebral L-proline uptake and that LQFM215 promotes neuroprotection and neuro-repair in the acute ischemic stroke model.
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Folacci M, Estaran S, Ménard C, Bertaud A, Rousset M, Roussel J, Thibaud JB, Vignes M, Chavanieu A, Charnet P, Cens T. Functional Characterization of Four Known Cav2.1 Variants Associated with Neurodevelopmental Disorders. MEMBRANES 2023; 13:96. [PMID: 36676903 PMCID: PMC9864995 DOI: 10.3390/membranes13010096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/06/2023] [Accepted: 01/09/2023] [Indexed: 06/17/2023]
Abstract
Cav2.1 channels are expressed throughout the brain and are the predominant Ca2+ channels in the Purkinje cells. These cerebellar neurons fire spontaneously, and Cav2.1 channels are involved in the regular pacemaking activity. The loss of precision of the firing pattern of Purkinje cells leads to ataxia, a disorder characterized by poor balance and difficulties in performing coordinated movements. In this study, we aimed at characterizing functional and structural consequences of four variations (p.A405T in I-II loop and p.R1359W, p.R1667W and p.S1799L in IIIS4, IVS4, and IVS6 helices, respectively) identified in patients exhibiting a wide spectrum of disorders including ataxia symptoms. Functional analysis using two major Cav2.1 splice variants (Cav2.1+e47 and Cav2.1-e47) in Xenopus laevis oocytes, revealed a lack of effect upon A405T substitution and a significant loss-of-function caused by R1359W, whereas R1667W and S1799L caused both channel gain-of-function and loss-of-function, in a splice variant-dependent manner. Structural analysis revealed the loss of interactions with S1, S2, and S3 helices upon R1359W and R1667W substitutions, but a lack of obvious structural changes with S1799L. Computational modeling suggests that biophysical changes induced by Cav2.1 pathogenic mutations might affect action potential frequency in Purkinje cells.
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Matamoros-Recio A, Mínguez-Toral M, Martín-Santamaría S. Modeling of Transmembrane Domain and Full-Length TLRs in Membrane Models. Methods Mol Biol 2023; 2700:3-38. [PMID: 37603172 DOI: 10.1007/978-1-0716-3366-3_1] [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: 08/22/2023]
Abstract
Toll-like receptors (TLRs), classified as pattern recognition receptors, have a primordial role in the activation of the innate immunity. In particular, TLR4 binds to lipopolysaccharides (LPS), a membrane constituent of Gram-negative bacteria, and, together with Myeloid Differentiation factor 2 (MD-2) protein, forms a heterodimeric complex which leads to the activation of the innate immune system response. Identification of TLRs has sparked great interest in the therapeutic manipulation of the innate immune system. In particular, TLR4 antagonists may be useful for the treatment of septic shock, certain autoimmune diseases, noninfectious inflammatory disorders, and neuropathic pain, and TLR4 agonists are under development as vaccine adjuvants in antitumoral treatments. Therefore, TLR4 has risen as a promising therapeutic target, and its modulation constitutes a highly relevant and active research area. Deep structural understanding of TLR4 signaling may help in the design and discovery of TLR4-modulating molecules with desirable therapeutic properties.Computational studies of the different independent domains composing the TLR4 were undertaken, to understand the differential domain organization of TLR4 in aqueous and membrane environments, including Liquid-disordered (Ld) and Liquid-ordered (Lo) membrane models, to account for the TLR4 recruitment in lipid rafts over activation. We modeled, by means of all-atom Molecular Dynamics (MD) simulations, the structural assembly of plausible full-length TLR4 models embedded into a realistic plasma membrane, accounting for the active (agonist) state of the TLR4, thus providing an analysis at both atomic/molecular and thermodynamic levels of the TLR4 assembly and biological activity. Our results unveil relevant molecular aspects involved in the mechanism of receptor activation, and adaptor recruitment in the innate immune pathways, and will promote the discovery of new TLR4 modulators and probes.
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Affiliation(s)
- Alejandra Matamoros-Recio
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas, CIB-CSIC, Madrid, Spain
| | - Marina Mínguez-Toral
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas, CIB-CSIC, Madrid, Spain
| | - Sonsoles Martín-Santamaría
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas, CIB-CSIC, Madrid, Spain.
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Bartuzi D, Kaczor AA, Matosiuk D. Illuminating the "Twilight Zone": Advances in Difficult Protein Modeling. Methods Mol Biol 2023; 2627:25-40. [PMID: 36959440 DOI: 10.1007/978-1-0716-2974-1_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Abstract
Homology modeling was long considered a method of choice in tertiary protein structure prediction. However, it used to provide models of acceptable quality only when templates with appreciable sequence identity with a target could be found. The threshold value was long assumed to be around 20-30%. Below this level, obtained sequence identity was getting dangerously close to values that can be obtained by chance, after aligning any random, unrelated sequences. In these cases, other approaches, including ab initio folding simulations or fragment assembly, were usually employed. The most recent editions of the CASP and CAMEO community-wide modeling methods assessment have brought some surprising outcomes, proving that much more clues can be inferred from protein sequence analyses than previously thought. In this chapter, we focus on recent advances in the field of difficult protein modeling, pushing the threshold deep into the "twilight zone", with particular attention devoted to improvements in applications of machine learning and model evaluation.
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Affiliation(s)
- Damian Bartuzi
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modelling Laboratory, Medical University of Lublin, Lublin, Poland.
| | - Agnieszka A Kaczor
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modelling Laboratory, Medical University of Lublin, Lublin, Poland
- University of Eastern Finland, School of Pharmacy, Kuopio, Finland
| | - Dariusz Matosiuk
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modelling Laboratory, Medical University of Lublin, Lublin, Poland
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30
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Evadgian A, Bharatha A, Cohall D. Use of Cheminformatics to Determine Potential Drug Interactions between Popular Barbadian Botanical Medicines and Antihypertensive Drugs. ACS OMEGA 2022; 7:44603-44619. [PMID: 36530331 PMCID: PMC9753521 DOI: 10.1021/acsomega.2c02446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 10/21/2022] [Indexed: 06/17/2023]
Abstract
Barbados has a rich traditional use of medicinal plants, especially among the older population who may have a chronic noncommunicable disease. This study aims to identify possible drug-herb interactions between popular herbal remedies used to manage elevated blood pressure and conventional antihypertensive drugs. In this study, in silico molecular docking experiments with AutoDock Vina (Scripps Research Institute, La Jolla, CA), a part of Yasara Structure software, version 20.12.24, were used to screen 30 potential phytochemicals for drug interactions from 11 popular plants in Barbados that are used for high blood pressure and could influence the pharmacology of the most prescribed antihypertensive drugs in Barbados. Thiazide and thiazide-like diuretics, calcium channel blockers (CCBs), angiotensin-converting enzyme inhibitors (ACE-I), and angiotensin receptor blockers (ARBs) are the most prescribed antihypertensive drugs. Twenty-seven phytochemicals show dissociation constants (K d) < 10 μM with pharmacological drug targets. Catharanthus roseus (L.) G. Don, Phyllanthus niruri L., Petroselinum crispum (Mill.) Fuss, and Lantana involucrata L. contain various compounds that show high binding affinities in all experiments. Possible interactions could affect renal excretion (thiazide-like diuretics), CYP metabolism (CCBs), absorption (ACE-I), hepatic CYP, and phase II metabolism (ARB). Oleanolic acid shows high binding affinities to almost all protein targets. This study also reveals potential candidates for the drug targets: T-type Cav3.3 (psychiatric diseases), PEPT1/2 (influencing bioavailability), and BK channel (epilepsy). Twenty-seven of 30 phytochemicals from C. roseus (L.) G. Don (Madagascar periwinkle), P. niruri L. (Seed under leaf), P. crispum Mill. Fuss (Parsley), and L. involucrata L. (Rock sage) have potential binding affinities with pharmacological targets of frequently prescribed antihypertensive drugs in Barbados and are likely to cause drug interactions. Compounds that are similar to naringin (e.g., astragalin, rutin, and quercitrin) and compounds that bind to OATP1, PEPT1/2, and enzymes involved in the metabolism of CCBs may be clinically relevant for further research. There should be greater awareness of potential drug-herb interactions, and further in vitro and in vivo studies are needed to unravel the exact effects on the pharmacology.
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Affiliation(s)
- Andraniek Evadgian
- Department
of Pharmaceutical Sciences, Utrecht University, David de Wied Building, Universiteitweg
99, 3584 CG Utrecht, The Netherlands
| | - Ambadasu Bharatha
- Department
of Preclinical and Health Sciences, Faculty of Medical Sciences, The University of the West Indies, Cave Hill Campus, BB14000 St. Michael, Barbados
| | - Damian Cohall
- Department
of Preclinical and Health Sciences, Faculty of Medical Sciences, The University of the West Indies, Cave Hill Campus, BB14000 St. Michael, Barbados
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31
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Farhana R, Lei R, Pham K, Derrien V, Cedeño J, Rodriquez V, Bernad S, Lima FF, Miksovska J. Globin X: A highly stable intrinsically hexacoordinate globin. J Inorg Biochem 2022; 236:111976. [PMID: 36058051 DOI: 10.1016/j.jinorgbio.2022.111976] [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: 06/29/2022] [Revised: 08/10/2022] [Accepted: 08/18/2022] [Indexed: 12/15/2022]
Abstract
Several novel members of the vertebrate globin family were recently discovered with unique structural features that are not found in traditional penta-coordinate globins. Here we combine structural tools to better understand and recognize molecular determinants that contribute to the stability of hexacoordinate globin X (GbX) from Danio rerio (zebrafish). pH-induced unfolding data indicates increased stability of GbX with pHmid of 1.9 ± 0.1 for met GbXWT, 2.4 ± 0.1 for met GbXC65A, and 3.4 ± 0.1 for GbXH90V. These results are in good agreement with GbX unfolding experiments using GuHCl, where a ΔGunf 13.8 ± 2.5 kcal mol-1 and 16.3 ± 2.6 kcal mol-1 are observed for metGbXWT, and metGbXC65A constructs, respectively, and diminished stability is measured for GbXH90V, ΔGunf = 9.5 ± 3.6 kcal mol-1. The metGbXWT and metGbXC65A also exhibit high thermal stability (melting points of 118 °C and 107 °C, respectively). Native ion mobility - mass spectrometry (IM-MS) experiments showed a narrow charge state distribution (9-12+) characteristics of a native, structured protein; a single mobility band was observed for the native states. Collision induced unfolding IM-MS experiments showed a two-state transition, in good agreement with the solution studies. GbXWT retains the heme over a wide range of charge states, suggesting strong interactions between the prosthetic group and the apoprotein. The above results indicate that in addition to the disulfide bond and the heme iron hexa-coordination, other structural determinants enhance stability of this protein.
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Affiliation(s)
- Rifat Farhana
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, United States of America
| | - Ruipeng Lei
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, United States of America
| | - Khoa Pham
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, United States of America
| | - Valerie Derrien
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, UMR8000, 91405 Orsay, France
| | - Jonathan Cedeño
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, United States of America
| | - Veronica Rodriquez
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, United States of America
| | - Sophie Bernad
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, UMR8000, 91405 Orsay, France
| | - Francisco Fernandez Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, United States of America; Biomedical Science Institute, Florida International University, Miami, FL, United States of America
| | - Jaroslava Miksovska
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, United States of America; Biomedical Science Institute, Florida International University, Miami, FL, United States of America.
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Shamkh IM, Al-Majidi M, Shntaif AH, Deng Kai PT, Nh-Pham N, Rahman I, Hamza D, Khan MS, Elsharayidi MS, Salah ET, Haikal A, Omoniyi MA, Abdalrahman MA, Karpinski TM. Nontoxic and Naturally Occurring Active Compounds as Potential Inhibitors of Biological Targets in Liriomyza trifolii. Int J Mol Sci 2022; 23:12791. [PMID: 36361586 PMCID: PMC9657120 DOI: 10.3390/ijms232112791] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 10/15/2022] [Accepted: 10/17/2022] [Indexed: 12/07/2023] Open
Abstract
In recent years, novel strategies to control insects have been based on protease inhibitors (PIs). In this regard, molecular docking and molecular dynamics simulations have been extensively used to investigate insect gut proteases and the interactions of PIs for the development of resistance against insects. We, herein, report an in silico study of (disodium 5'-inosinate and petunidin 3-glucoside), (calcium 5'-guanylate and chlorogenic acid), chlorogenic acid alone, (kaempferol-3,7-di-O-glucoside with hyperoside and delphinidin 3-glucoside), and (myricetin 3'-glucoside and hyperoside) as potential inhibitors of acetylcholinesterase receptors, actin, α-tubulin, arginine kinase, and histone receptor III subtypes, respectively. The study demonstrated that the inhibitors are capable of forming stable complexes with the corresponding proteins while also showing great potential for inhibitory activity in the proposed protein-inhibitor combinations.
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Affiliation(s)
- Israa M. Shamkh
- Botany and Microbiology Department, Faculty of Science, Cairo University, Cairo 12613, Egypt
- Chemo and Bioinformatics Lab, Bio Search Research Institution, BSRI, Giza 12613, Egypt
| | - Mohammed Al-Majidi
- Department of Chemistry, College of Science for Women, University of Babylon, Alhilla 51002, Iraq
| | - Ahmed Hassen Shntaif
- Department of Chemistry, College of Science for Women, University of Babylon, Alhilla 51002, Iraq
| | - Peter Tan Deng Kai
- Victoria Junior College, Crimson Research Institute, Singapore 449035, Singapore
| | - Ngoc Nh-Pham
- Department of Biotechnology, Faculty of Biology and Biotechnology, VNU-HCM University of Science, Ho Chi Minh City 700000, Vietnam
| | - Ishrat Rahman
- Department of Basic Dental Sciences, College of Dentistry, Princess Nourah bint Abdulrahman University, Riyadh 11564, Saudi Arabia
| | - Dalia Hamza
- Zoonoses Department, Faculty of Veterinary Medicine, Cairo University, Giza 11221, Egypt
| | | | - Maii S. Elsharayidi
- Central Public Health Laboratories, Egyptian Ministry of Health, Cairo 11511, Egypt
| | - Eman T. Salah
- Biochemistry Department, Faculty of Science, Ain Shams University, Ain Shams 11591, Egypt
| | - Abdullah Haikal
- Department of Pharmacognosy, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | | | - Mahmoud A. Abdalrahman
- Science Department—Chemistry, Milton Academy, Crimson Research Institute, Milton, MA 02186, USA
| | - Tomasz M. Karpinski
- Chair and Department of Medical Microbiology, Poznań University of Medical Sciences, Wieniawskiego 3, 61-712 Poznań, Poland
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Holmes AOM, Goldman A, Kalli AC. mPPases create a conserved anionic membrane fingerprint as identified via multi-scale simulations. PLoS Comput Biol 2022; 18:e1010578. [PMID: 36191052 PMCID: PMC9560603 DOI: 10.1371/journal.pcbi.1010578] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 10/13/2022] [Accepted: 09/16/2022] [Indexed: 11/06/2022] Open
Abstract
Membrane-integral pyrophosphatases (mPPases) are membrane-bound enzymes responsible for hydrolysing inorganic pyrophosphate and translocating a cation across the membrane. Their function is essential for the infectivity of clinically relevant protozoan parasites and plant maturation. Recent developments have indicated that their mechanism is more complicated than previously thought and that the membrane environment may be important for their function. In this work, we use multiscale molecular dynamics simulations to demonstrate for the first time that mPPases form specific anionic lipid interactions at 4 sites at the distal and interfacial regions of the protein. These interactions are conserved in simulations of the mPPases from Thermotoga maritima, Vigna radiata and Clostridium leptum and characterised by interactions with positive residues on helices 1, 2, 3 and 4 for the distal site, or 9, 10, 13 and 14 for the interfacial site. Due to the importance of these helices in protein stability and function, these lipid interactions may play a crucial role in the mPPase mechanism and enable future structural and functional studies.
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Affiliation(s)
- Alexandra O. M. Holmes
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Adrian Goldman
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
- Research Program in Molecular and Integrative Biosciences, University of Helsinki, Helsinki, Finland
| | - Antreas C. Kalli
- Leeds Institute of Cardiovascular and Metabolic Medicine and Astbury Centre for Structural Biology, University of Leeds, Leeds, United Kingdom
- * E-mail:
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34
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In Silico Evaluation of Hexamethylene Amiloride Derivatives as Potential Luminal Inhibitors of SARS-CoV-2 E Protein. Int J Mol Sci 2022; 23:ijms231810647. [PMID: 36142556 PMCID: PMC9503309 DOI: 10.3390/ijms231810647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/01/2022] [Accepted: 09/01/2022] [Indexed: 11/24/2022] Open
Abstract
The coronavirus E proteins are small membrane proteins found in the virus envelope of alpha and beta coronaviruses that have a high degree of overlap in their biochemical and functional properties despite minor sequence variations. The SARS-CoV-2 E is a 75-amino acid transmembrane protein capable of acting as an ion channel when assembled in a pentameric fashion. Various studies have found that hexamethylene amiloride (HMA) can inhibit the ion channel activity of the E protein in bilayers and also inhibit viral replication in cultured cells. Here, we use the available structural data in conjunction with homology modelling to build a comprehensive model of the E protein to assess potential binding sites and molecular interactions of HMA derivatives. Furthermore, we employed an iterative cycle of molecular modelling, extensive docking simulations, molecular dynamics and leveraging steered molecular dynamics to better understand the pore characteristics and quantify the affinity of the bound ligands. Results from this work highlight the potential of acylguanidines as blockers of the E protein and guide the development of subsequent small molecule inhibitors.
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35
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Liang YY, Yan LQ, Tan MH, Li GH, Fang JH, Peng JY, Li KT. Isolation, characterization, and genome sequencing of a novel chitin deacetylase producing Bacillus aryabhattai TCI-16. Front Microbiol 2022; 13:999639. [PMID: 36171752 PMCID: PMC9511218 DOI: 10.3389/fmicb.2022.999639] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 08/23/2022] [Indexed: 11/23/2022] Open
Abstract
Chitin deacetylase (CDA) is a chitin degradation enzyme that catalyzes the conversion of chitin to chitosan by the deacetylation of N-acetyl-D-glucosamine residues, playing an important role in the high-value utilization of waste chitin. The shells of shrimp and crab are rich in chitin, and mangroves are usually recognized as an active habitat to shrimp and crab. In the present study, a CDA-producing bacterium, strain TCI-16, was isolated and screened from the mangrove soil. Strain TCI-16 was identified and named as Bacillus aryabhattai TCI-16, and the maximum CDA activity in fermentation broth reached 120.35 ± 2.40 U/mL at 36 h of cultivation. Furthermore, the complete genome analysis of B. aryabhattai TCI-16 revealed the chitin-degrading enzyme system at genetic level, in which a total of 13 putative genes were associated with carbohydrate esterase 4 (CE4) family enzymes, including one gene coding CDA, seven genes encoding polysaccharide deacetylases, and five genes encoding peptidoglycan-N-acetyl glucosamine deacetylases. Amino acid sequence analysis showed that the predicted CDA of B. aryabhattai TCI-16 was composed of 236 amino acid residues with a molecular weight of 27.3 kDa, which possessed a conserved CDA active like the known CDAs. However, the CDA of B. aryabhattai TCI-16 showed low homology (approximately 30%) with other microbial CDAs, and its phylogenetic tree belonged to a separate clade in bacteria, suggesting a high probability in structural novelty. In conclusion, the present study indicated that the novel CDA produced by B. aryabhattai TCI-16 might be a promising option for bioconversion of chitin to the value-added chitosan.
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Affiliation(s)
- Ying-yin Liang
- Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Provincial Engineering Technology Research Center of Seafood, Guangdong Province Engineering Laboratory for Marine Biological Products, College of Food Science and Technology, Key Laboratory of Advanced Processing of Aquatic Product of Guangdong Higher Education Institution, Guangdong Ocean University, Zhanjiang, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
| | - Lu-qi Yan
- Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Provincial Engineering Technology Research Center of Seafood, Guangdong Province Engineering Laboratory for Marine Biological Products, College of Food Science and Technology, Key Laboratory of Advanced Processing of Aquatic Product of Guangdong Higher Education Institution, Guangdong Ocean University, Zhanjiang, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
| | - Ming-hui Tan
- Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Provincial Engineering Technology Research Center of Seafood, Guangdong Province Engineering Laboratory for Marine Biological Products, College of Food Science and Technology, Key Laboratory of Advanced Processing of Aquatic Product of Guangdong Higher Education Institution, Guangdong Ocean University, Zhanjiang, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
| | - Gang-hui Li
- Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Provincial Engineering Technology Research Center of Seafood, Guangdong Province Engineering Laboratory for Marine Biological Products, College of Food Science and Technology, Key Laboratory of Advanced Processing of Aquatic Product of Guangdong Higher Education Institution, Guangdong Ocean University, Zhanjiang, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
| | - Jian-hao Fang
- Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Provincial Engineering Technology Research Center of Seafood, Guangdong Province Engineering Laboratory for Marine Biological Products, College of Food Science and Technology, Key Laboratory of Advanced Processing of Aquatic Product of Guangdong Higher Education Institution, Guangdong Ocean University, Zhanjiang, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
| | - Jie-ying Peng
- Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Provincial Engineering Technology Research Center of Seafood, Guangdong Province Engineering Laboratory for Marine Biological Products, College of Food Science and Technology, Key Laboratory of Advanced Processing of Aquatic Product of Guangdong Higher Education Institution, Guangdong Ocean University, Zhanjiang, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
| | - Kun-tai Li
- Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Provincial Engineering Technology Research Center of Seafood, Guangdong Province Engineering Laboratory for Marine Biological Products, College of Food Science and Technology, Key Laboratory of Advanced Processing of Aquatic Product of Guangdong Higher Education Institution, Guangdong Ocean University, Zhanjiang, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
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36
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Bitton M, Keasar C. Estimation of model accuracy by a unique set of features and tree-based regressor. Sci Rep 2022; 12:14074. [PMID: 35982086 PMCID: PMC9388490 DOI: 10.1038/s41598-022-17097-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 07/20/2022] [Indexed: 11/26/2022] Open
Abstract
Computationally generated models of protein structures bridge the gap between the practically negligible price tag of sequencing and the high cost of experimental structure determination. By providing a low-cost (and often free) partial alternative to experimentally determined structures, these models help biologists design and interpret their experiments. Obviously, the more accurate the models the more useful they are. However, methods for protein structure prediction generate many structural models of various qualities, necessitating means for the estimation of their accuracy. In this work we present MESHI_consensus, a new method for the estimation of model accuracy. The method uses a tree-based regressor and a set of structural, target-based, and consensus-based features. The new method achieved high performance in the EMA (Estimation of Model Accuracy) track of the recent CASP14 community-wide experiment (https://predictioncenter.org/casp14/index.cgi). The tertiary structure prediction track of that experiment revealed an unprecedented leap in prediction performance by a single prediction group/method, namely AlphaFold2. This achievement would inevitably have a profound impact on the field of protein structure prediction, including the accuracy estimation sub-task. We conclude this manuscript with some speculations regarding the future role of accuracy estimation in a new era of accurate protein structure prediction.
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Affiliation(s)
- Mor Bitton
- Department of Computer Science, Ben Gurion University, Be'er Sheva, Israel.
| | - Chen Keasar
- Department of Computer Science, Ben Gurion University, Be'er Sheva, Israel.
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37
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Pervaiz I, Zahra FT, Mikelis C, Al-Ahmad AJ. An in vitro model of glucose transporter 1 deficiency syndrome at the blood-brain barrier using induced pluripotent stem cells. J Neurochem 2022; 162:483-500. [PMID: 35943296 DOI: 10.1111/jnc.15684] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 07/08/2022] [Accepted: 08/03/2022] [Indexed: 11/28/2022]
Abstract
Glucose is an important source of energy for the central nervous system. Its uptake at the blood-brain barrier (BBB) is mostly mediated via glucose transporter 1 (GLUT1), a facilitated transporter encoded by the SLC2A1 gene. GLUT1 Deficiency Syndrome (GLUT1DS) is a haploinsufficiency characterized by mutations in the SLC2A1 gene, resulting in impaired glucose uptake at the BBB and clinically characterized by epileptic seizures and movement disorder. A major limitation is an absence of in vitro models of the BBB reproducing the disease. This study aimed to characterize an in vitro model of GLUT1DS using human pluripotent stem cells (iPSCs). Two GLUT1DS clones were generated (GLUT1-iPSC) from their original parental clone iPS(IMR90)-c4 by CRISPR/Cas9 and differentiated into brain microvascular endothelial cells (iBMECs). Cells were characterized in terms of SLC2A1 expression, changes in the barrier function, glucose uptake and metabolism, and angiogenesis. GLUT1DS iPSCs and iBMECs showed comparable phenotype to their parental control, with exception of reduced GLUT1 expression at the protein level. Although no major disruption in the barrier function was reported in the two clones, a significant reduction in glucose uptake accompanied by an increase in glycolysis and mitochondrial respiration was reported in both GLUT1DS-iBMECs. Finally, impaired angiogenic features were reported in such clones compared to the parental clone. Our study provides the first documented characterization of GLUT1DS-iBMECs generated by CRISPR-Cas9, suggesting that GLUT1 truncation appears detrimental to brain angiogenesis and brain endothelial bioenergetics, but maybe not be detrimental to iBMECs differentiation and barriergenesis. Our future direction is to further characterize the functional outcome of such truncated product, as well as its impact on other cells of the neurovascular unit.
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Affiliation(s)
- Iqra Pervaiz
- Texas Tech University Health Sciences Center, Jerry H. Hodge School of Pharmacy, Department of Pharmaceutical Sciences, Amarillo, Texas, United States of America
| | - Fatema Tuz Zahra
- Texas Tech University Health Sciences Center, Jerry H. Hodge School of Pharmacy, Department of Pharmaceutical Sciences, Amarillo, Texas, United States of America
| | - Constantinos Mikelis
- Texas Tech University Health Sciences Center, Jerry H. Hodge School of Pharmacy, Department of Pharmaceutical Sciences, Amarillo, Texas, United States of America
| | - Abraham Jacob Al-Ahmad
- Texas Tech University Health Sciences Center, Jerry H. Hodge School of Pharmacy, Department of Pharmaceutical Sciences, Amarillo, Texas, United States of America
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38
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Mahtarin R, Islam S, Islam MJ, Ullah MO, Ali MA, Halim MA. Structure and dynamics of membrane protein in SARS-CoV-2. J Biomol Struct Dyn 2022; 40:4725-4738. [PMID: 33353499 PMCID: PMC7784837 DOI: 10.1080/07391102.2020.1861983] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 12/05/2020] [Indexed: 12/15/2022]
Abstract
SARS-CoV-2 membrane (M) protein performs a variety of critical functions in virus infection cycle. However, the expression and purification of membrane protein structure is difficult despite tremendous progress. In this study, the 3 D structure is modeled followed by intensive validation and molecular dynamics simulation. The lack of suitable homologous templates (>30% sequence identities) leads us to construct the membrane protein models using template-free modeling (de novo or ab initio) approach with Robetta and trRosetta servers. Comparing with other model structures, it is evident that trRosetta (TM-score: 0.64; TM region RMSD: 2 Å) can provide the best model than Robetta (TM-score: 0.61; TM region RMSD: 3.3 Å) and I-TASSER (TM-score: 0.45; TM region RMSD: 6.5 Å). 100 ns molecular dynamics simulations are performed on the model structures by incorporating membrane environment. Moreover, secondary structure elements and principal component analysis (PCA) have also been performed on MD simulation data. Finally, trRosetta model is utilized for interpretation and visualization of interacting residues during protein-protein interactions. The common interacting residues including Phe103, Arg107, Met109, Trp110, Arg131, and Glu135 in the C-terminal domain of M protein are identified in membrane-spike and membrane-nucleocapsid protein complexes. The active site residues are also predicted for potential drug and peptide binding. Overall, this study might be helpful to design drugs and peptides against the modeled membrane protein of SARS-CoV-2 to accelerate further investigation. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rumana Mahtarin
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Shafiqul Islam
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Md. Jahirul Islam
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - M Obayed Ullah
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Md Ackas Ali
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Mohammad A. Halim
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
- Department of Physical Sciences, University of Arkansas - Fort Smith, Fort Smith, AR, USA
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López-Rivera JJ, Rodríguez-Salazar L, Soto-Ospina A, Estrada-Serrato C, Serrano D, Chaparro-Solano HM, Londoño O, Rueda PA, Ardila G, Villegas-Lanau A, Godoy-Corredor M, Cuartas M, Vélez JI, Vidal OM, Isaza-Ruget MA, Arcos-Burgos M. Structural Protein Effects Underpinning Cognitive Developmental Delay of the PURA p.Phe233del Mutation Modelled by Artificial Intelligence and the Hybrid Quantum Mechanics–Molecular Mechanics Framework. Brain Sci 2022; 12:brainsci12070871. [PMID: 35884678 PMCID: PMC9313109 DOI: 10.3390/brainsci12070871] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/21/2022] [Accepted: 06/24/2022] [Indexed: 02/06/2023] Open
Abstract
A whole-exome capture and next-generation sequencing was applied to an 11 y/o patient with a clinical history of congenital hypotonia, generalized motor and cognitive neurodevelopmental delay, and severe cognitive deficit, and without any identifiable Syndromic pattern, and to her parents, we disclosed a de novo heterozygous pathogenic mutation, c.697_699del p.Phe233del (rs786204835)(ACMG classification PS2, PM1, PM2, PP5), harbored in the PURA gene (MIM*600473) (5q31.3), associated with Autosomal Dominant Mental Retardation 31 (MIM # 616158). We used the significant improvement in the accuracy of protein structure prediction recently implemented in AlphaFold that incorporates novel neural network architectures and training procedures based on the evolutionary, physical, and geometric constraints of protein structures. The wild-type (WT) sequence and the mutated sequence, missing the Phe233, were reconstructed. The predicted local Distance Difference Test (lDDT) for the PURAwt and the PURA–Phe233del showed that the occurrence of the Phe233del affects between 220–320 amino acids. The distortion in the PURA structural conformation in the ~5 Å surrounding area after the p.Phe233del produces a conspicuous disruption of the repeat III, where the DNA and RNA helix unwinding capability occurs. PURA Protein–DNA docking corroborated these results in an in silico analysis that showed a loss of the contact of the PURA–Phe233del III repeat domain model with the DNA. Together, (i) the energetic and stereochemical, (ii) the hydropathic indexes and polarity surfaces, and (iii) the hybrid Quantum Mechanics–Molecular Mechanics (QM–MM) analyses of the PURA molecular models demarcate, at the atomic resolution, the specific surrounding region affected by these mutations and pave the way for future cell-based functional analysis. To the best of our knowledge, this is the first report of a de novo mutation underpinning a PURA syndrome in a Latin American patient and highlights the importance of predicting the molecular effects in protein structure using artificial intelligence algorithms and molecular and atomic resolution stereochemical analyses.
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Affiliation(s)
- Juan Javier López-Rivera
- INPAC Research Group, Fundación Universitaria Sanitas, Bogotá 111321, Colombia;
- Grupo de Genética Médica, Clínica Universitaria Colombia y Clínica Pediátrica Colsanitas, Bogotá 111321, Colombia; (C.E.-S.); (D.S.); (H.M.C.-S.); (O.L.)
- Correspondence: (J.J.L.-R.); (M.A.-B.)
| | - Luna Rodríguez-Salazar
- Grupo de Bioinformática, Laboratorio de Clínica Colsanitas, Bogotá 110221, Colombia; (L.R.-S.); (P.A.R.); (G.A.)
| | - Alejandro Soto-Ospina
- Genética Molecular (GenMol), Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia, Medellín 050012, Colombia; (A.S.-O.); (A.V.-L.)
| | - Carlos Estrada-Serrato
- Grupo de Genética Médica, Clínica Universitaria Colombia y Clínica Pediátrica Colsanitas, Bogotá 111321, Colombia; (C.E.-S.); (D.S.); (H.M.C.-S.); (O.L.)
| | - David Serrano
- Grupo de Genética Médica, Clínica Universitaria Colombia y Clínica Pediátrica Colsanitas, Bogotá 111321, Colombia; (C.E.-S.); (D.S.); (H.M.C.-S.); (O.L.)
| | - Henry Mauricio Chaparro-Solano
- Grupo de Genética Médica, Clínica Universitaria Colombia y Clínica Pediátrica Colsanitas, Bogotá 111321, Colombia; (C.E.-S.); (D.S.); (H.M.C.-S.); (O.L.)
| | - Olga Londoño
- Grupo de Genética Médica, Clínica Universitaria Colombia y Clínica Pediátrica Colsanitas, Bogotá 111321, Colombia; (C.E.-S.); (D.S.); (H.M.C.-S.); (O.L.)
| | - Paula A. Rueda
- Grupo de Bioinformática, Laboratorio de Clínica Colsanitas, Bogotá 110221, Colombia; (L.R.-S.); (P.A.R.); (G.A.)
| | - Geraldine Ardila
- Grupo de Bioinformática, Laboratorio de Clínica Colsanitas, Bogotá 110221, Colombia; (L.R.-S.); (P.A.R.); (G.A.)
| | - Andrés Villegas-Lanau
- Genética Molecular (GenMol), Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia, Medellín 050012, Colombia; (A.S.-O.); (A.V.-L.)
- Grupo de Neurociencias de Antioquia (GNA), Facultad de Medicina, Universidad de Antioquia, Medellín 050012, Colombia
| | | | - Mauricio Cuartas
- Grupo de Investigación Estudios en Psicología, Departamento de Psicología, Escuela de Humanidades, Universidad EAFIT, Medellín 050022, Colombia;
| | - Jorge I. Vélez
- Universidad del Norte, Barranquilla 080001, Colombia; (J.I.V.); (O.M.V.)
| | - Oscar M. Vidal
- Universidad del Norte, Barranquilla 080001, Colombia; (J.I.V.); (O.M.V.)
| | | | - Mauricio Arcos-Burgos
- Grupo de Investigación en Psiquiatría (GIPSI), Departamento de Psiquiatría, Instituto de Investigaciones Médicas, Facultad de Medicina, Universidad de Antioquia, Medellín 050012, Colombia
- Correspondence: (J.J.L.-R.); (M.A.-B.)
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Llanos MA, Enrique N, Sbaraglini ML, Garofalo FM, Talevi A, Gavernet L, Martín P. Structure-Based Virtual Screening Identifies Novobiocin, Montelukast, and Cinnarizine as TRPV1 Modulators with Anticonvulsant Activity In Vivo. J Chem Inf Model 2022; 62:3008-3022. [PMID: 35696534 DOI: 10.1021/acs.jcim.2c00312] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The transient receptor potential vanilloid 1 (TRPV1) receptor is a nonselective cation channel, known to be involved in the regulation of many important physiological and pathological processes. In the last few years, it has been proposed as a promising target to develop novel anticonvulsant compounds. However, thermoregulatory effects associated with the channel inhibition have hampered the path for TRPV1 antagonists to become marketed drugs. In this regard, we conducted a structure-based virtual screening campaign to find potential TRPV1 modulators among approved drugs, which are known to be safe and thermally neutral. To this end, different docking models were developed and validated by assessing their pose and score prediction powers. Novobiocin, montelukast, and cinnarizine were selected from the screening as promising candidates for experimental testing and all of them exhibited nanomolar inhibitory activity. Moreover, the in vivo profiles showed promising results in at least one of the three models of seizures tested.
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Affiliation(s)
- Manuel A Llanos
- Departamento de Ciencias Biológicas and Laboratorio de Investigación y Desarrollo de Bioactivos (LIDeB), UNLP, Facultad de Ciencias Exactas, La Plata Buenos Aires (B1900ADU), Argentina
| | - Nicolás Enrique
- Instituto de Estudios Inmunológicos y Fisiopatológicos (IIFP, CONICET─Universidad Nacional de la Plata), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata Buenos Aires (B1900BJW), Argentina
| | - María L Sbaraglini
- Departamento de Ciencias Biológicas and Laboratorio de Investigación y Desarrollo de Bioactivos (LIDeB), UNLP, Facultad de Ciencias Exactas, La Plata Buenos Aires (B1900ADU), Argentina
| | - Federico M Garofalo
- Departamento de Ciencias Biológicas and Laboratorio de Investigación y Desarrollo de Bioactivos (LIDeB), UNLP, Facultad de Ciencias Exactas, La Plata Buenos Aires (B1900ADU), Argentina
| | - Alan Talevi
- Departamento de Ciencias Biológicas and Laboratorio de Investigación y Desarrollo de Bioactivos (LIDeB), UNLP, Facultad de Ciencias Exactas, La Plata Buenos Aires (B1900ADU), Argentina
| | - Luciana Gavernet
- Departamento de Ciencias Biológicas and Laboratorio de Investigación y Desarrollo de Bioactivos (LIDeB), UNLP, Facultad de Ciencias Exactas, La Plata Buenos Aires (B1900ADU), Argentina
| | - Pedro Martín
- Instituto de Estudios Inmunológicos y Fisiopatológicos (IIFP, CONICET─Universidad Nacional de la Plata), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata Buenos Aires (B1900BJW), Argentina
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Gain and loss of TASK3 channel function and its regulation by novel variation cause KCNK9 imprinting syndrome. Genome Med 2022; 14:62. [PMID: 35698242 PMCID: PMC9195326 DOI: 10.1186/s13073-022-01064-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 05/19/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genomics enables individualized diagnosis and treatment, but large challenges remain to functionally interpret rare variants. To date, only one causative variant has been described for KCNK9 imprinting syndrome (KIS). The genotypic and phenotypic spectrum of KIS has yet to be described and the precise mechanism of disease fully understood. METHODS This study discovers mechanisms underlying KCNK9 imprinting syndrome (KIS) by describing 15 novel KCNK9 alterations from 47 KIS-affected individuals. We use clinical genetics and computer-assisted facial phenotyping to describe the phenotypic spectrum of KIS. We then interrogate the functional effects of the variants in the encoded TASK3 channel using sequence-based analysis, 3D molecular mechanic and dynamic protein modeling, and in vitro electrophysiological and functional methodologies. RESULTS We describe the broader genetic and phenotypic variability for KIS in a cohort of individuals identifying an additional mutational hotspot at p.Arg131 and demonstrating the common features of this neurodevelopmental disorder to include motor and speech delay, intellectual disability, early feeding difficulties, muscular hypotonia, behavioral abnormalities, and dysmorphic features. The computational protein modeling and in vitro electrophysiological studies discover variability of the impact of KCNK9 variants on TASK3 channel function identifying variants causing gain and others causing loss of conductance. The most consistent functional impact of KCNK9 genetic variants, however, was altered channel regulation. CONCLUSIONS This study extends our understanding of KIS mechanisms demonstrating its complex etiology including gain and loss of channel function and consistent loss of channel regulation. These data are rapidly applicable to diagnostic strategies, as KIS is not identifiable from clinical features alone and thus should be molecularly diagnosed. Furthermore, our data suggests unique therapeutic strategies may be needed to address the specific functional consequences of KCNK9 variation on channel function and regulation.
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Incampo G, Giangregorio N, Gambacorta N, Nicolotti O, Pacifico C, Palmieri L, Tonazzi A. Praseodymium trivalent ion is an effective inhibitor of mitochondrial basic amino acids and carnitine/acylcarnitine carriers. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2022; 1863:148557. [PMID: 35367451 DOI: 10.1016/j.bbabio.2022.148557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/18/2022] [Accepted: 03/25/2022] [Indexed: 06/14/2023]
Abstract
We herein report the identification of the lantanide praseodymium trivalent ion Pr3+ as inhibitor of mitochondrial transporters for basic amino acids and phylogenetically related carriers belonging to the Slc25 family. The inhibitory effect of Pr3+ has been tested using mitochondrial transporters reconstituted into liposomes being effective in the micromolar range, acting as a competitive inhibitor of the human basic amino acids carrier (BAC, Slc25A29), the human carnitine/acylcarnitine carrier (CAC, Slc25A20). Furthermore, we provide computational evidence that the complete inhibition of the transport activity of the recombinant proteins is due to the Pr3+ coordination to key acidic residues of the matrix salt bridge network. Besides being used as a first choice stop inhibitor for functional studies in vitro of mitochondrial carriers reconstituted in proteoliposomes, Pr3+ might also represent a useful tool for structural studies of the mitochondrial carrier family.
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Affiliation(s)
- Giovanna Incampo
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via Orabona 4, 70125 Bari, Italy
| | - Nicola Giangregorio
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via Orabona 4, 70125 Bari, Italy; CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), Via Amendola 122/O, 70126 Bari, Italy
| | - Nicola Gambacorta
- Department of Pharmacy-Pharmaceutical Sciences, University of Bari, Via Orabona 4, 70125 Bari, Italy
| | - Orazio Nicolotti
- Department of Pharmacy-Pharmaceutical Sciences, University of Bari, Via Orabona 4, 70125 Bari, Italy
| | - Concetta Pacifico
- Department of Chemistry, University of Bari, Via Orabona 4, 70125 Bari, Italy
| | - Luigi Palmieri
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via Orabona 4, 70125 Bari, Italy; CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), Via Amendola 122/O, 70126 Bari, Italy
| | - Annamaria Tonazzi
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via Orabona 4, 70125 Bari, Italy; CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), Via Amendola 122/O, 70126 Bari, Italy.
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Ben Ayed R, Chirmade T, Hanana M, Khamassi K, Ercisli S, Choudhary R, Kadoo N, Karunakaran R. Comparative Analysis and Structural Modeling of Elaeis oleifera FAD2, a Fatty Acid Desaturase Involved in Unsaturated Fatty Acid Composition of American Oil Palm. BIOLOGY 2022; 11:529. [PMID: 35453727 PMCID: PMC9032008 DOI: 10.3390/biology11040529] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 03/13/2022] [Accepted: 03/23/2022] [Indexed: 11/17/2022]
Abstract
American oil palm (Elaeis oleifera) is an important source of dietary oil that could fulfill the increasing worldwide demand for cooking oil. Therefore, improving its production is crucial and could be realized through breeding and genetic engineering approaches aiming to obtain high-yielding varieties with improved oil content and quality. The fatty acid composition and particularly the oleic/linoleic acid ratio are major factors influencing oil quality. Our work focused on a fatty acid desaturase (FAD) enzyme involved in the desaturation and conversion of oleic acid to linoleic acid. Following the in silico identification and annotation of Elaeis oleifera FAD2, its molecular and structural features characterization was performed to better understand the mechanistic bases of its enzymatic activity. EoFAD2 is 1173 nucleotides long and encodes a protein of 390 amino acids that shares similarities with other FADs. Interestingly, the phylogenetic study showed three distinguished groups where EoFAD2 clustered among monocotyledonous taxa. EoFAD2 is a membrane-bound protein with five transmembrane domains presumably located in the endoplasmic reticulum. The homodimer organization model of EoFAD2 enzyme and substrates and respective substrate-binding residues were predicted and described. Moreover, the comparison between 24 FAD2 sequences from different species generated two interesting single-nucleotide polymorphisms (SNPs) associated with the oleic/linoleic acid contents.
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Affiliation(s)
- Rayda Ben Ayed
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Sidi Mansour Road, P.O. Box 1177, Sfax 3018, Tunisia
| | - Tejas Chirmade
- CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pashan, Pune 411008, India; (T.C.); (N.K.)
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Mohsen Hanana
- Laboratory of Extremophile Plants, Centre of Biotechnology of Borj-Cédria, B.P. 901, Hammam Lif 2050, Tunisia;
| | - Khalil Khamassi
- Field Crop Laboratory (LR16INRAT02), Institut National de la Recherche Agronomique de Tunisie (INRAT), University of Carthage, Tunis 1004, Tunisia;
| | - Sezai Ercisli
- Department of Horticulture, Faculty of Agriculture, Ataturk University, Erzurum 25240, Turkey;
| | - Ravish Choudhary
- Division of Seed Science and Technology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India;
| | - Narendra Kadoo
- CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pashan, Pune 411008, India; (T.C.); (N.K.)
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Rohini Karunakaran
- Unit of Biochemistry, Centre of Excellence for Biomaterials Engineering, Faculty of Medicine, AIMST University, Semeling, Bedong 08100, Malaysia
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Zimmermann MT. Molecular Modeling is an Enabling Approach to Complement and Enhance Channelopathy Research. Compr Physiol 2022; 12:3141-3166. [PMID: 35578963 DOI: 10.1002/cphy.c190047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Hundreds of human membrane proteins form channels that transport necessary ions and compounds, including drugs and metabolites, yet details of their normal function or how function is altered by genetic variants to cause diseases are often unknown. Without this knowledge, researchers are less equipped to develop approaches to diagnose and treat channelopathies. High-resolution computational approaches such as molecular modeling enable researchers to investigate channelopathy protein function, facilitate detailed hypothesis generation, and produce data that is difficult to gather experimentally. Molecular modeling can be tailored to each physiologic context that a protein may act within, some of which may currently be difficult or impossible to assay experimentally. Because many genomic variants are observed in channelopathy proteins from high-throughput sequencing studies, methods with mechanistic value are needed to interpret their effects. The eminent field of structural bioinformatics integrates techniques from multiple disciplines including molecular modeling, computational chemistry, biophysics, and biochemistry, to develop mechanistic hypotheses and enhance the information available for understanding function. Molecular modeling and simulation access 3D and time-dependent information, not currently predictable from sequence. Thus, molecular modeling is valuable for increasing the resolution with which the natural function of protein channels can be investigated, and for interpreting how genomic variants alter them to produce physiologic changes that manifest as channelopathies. © 2022 American Physiological Society. Compr Physiol 12:3141-3166, 2022.
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Affiliation(s)
- Michael T Zimmermann
- Bioinformatics Research and Development Laboratory, Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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Prabu R, Mohanty A, Balakrishnan SS, Jayalakshmi G, Sundar K. Molecular docking and simulation of IcaC protein as O-succinyltransferase function in staphylococcus epidermidis biofilm formation. Curr Res Struct Biol 2022; 4:78-86. [PMID: 35399651 PMCID: PMC8987812 DOI: 10.1016/j.crstbi.2022.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/19/2022] [Accepted: 03/13/2022] [Indexed: 12/04/2022] Open
Abstract
Intercellular adhesion (IcaADBC) operon is necessary for PNAG (Polyβ-1,6-N-acetyl-D-glucosamine) biosynthesis of biofilm formation in Staphylococcus epidermidis. IcaC protein has a wide range of functions in terms of growth phase variation, migration, transposon insertion, PNAG modification, biofilm formation. Unusual TTTA signature motifs were identified from nucleotide sequence. Asparagine-linked glycosylation consensus motifs were identified at position 169 and 240. S. epidermidis was a close evolutionary association with S. haemolyticus and other Staphylococcus spp. Due to the non-availability of crystal structure, protein threading procedure was selected for constructing a full length IcaC three-dimensional structure. QMEANBrane structure quality assessment with model scores −100000 range within predicted integral membrane structure. IcaC motif constitutes 18 transmembrane helix, 37 helix-helix interaction, 8 beta turn, 2 gamma turn. Binding free energy was calculated with their succinate ligand docking form hydrogen bond with critical amino acids showed ΔG score −2.574 kJ/mol using Schrödinger. Serine (Ser96), Glutamic acid (Glu99), Tryptophan (Trp191) were active site amino acids form the catalytic core required for O-succinyltransferase function. Molecular dynamics simulation (MDS) was performed to evaluate the stability of IcaC protein and IcaC-Succinate binding complexes with the active site amino acids throughout trajectories captured with time scale 100 ns simulation period using GROMACS 4.5. Structural characterization of Intercellular adhesion (IcaC) protein from Staphylococcus epidermidis. Understanding of nucleotide, protein signature sequence, secondary structure motifs and phylogenetic association among Staphylococcus sp. homologs. IcaC-Succinate docking and molecular dynamics simulation for determined structural stability of protein.
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Shi S, Pang C, Ren S, Sun F, Ma B, Guo S, Li J, Chen Y, An H. Molecular dynamics simulation of TMEM16A channel: Linking structure with gating. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183777. [PMID: 34537214 DOI: 10.1016/j.bbamem.2021.183777] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 08/23/2021] [Accepted: 09/12/2021] [Indexed: 10/20/2022]
Abstract
TMEM16A, the calcium-activated chloride channel, is broadly expressed and plays pivotal roles in diverse physiological processes. To understand the structural and functional relationships of TMEM16A, it is necessary to fully clarify the structural basis of the gating of the TMEM16A channel. Herein, we performed the protein electrostatic analysis and molecular dynamics simulation on the TMEM16A in the presence and absence of Ca2+. Data showed that the separation of TM4 and TM6 causes pore expansion, and Q646 may be a key residue for the formation of π-helix in the middle segment of TM6. Moreover, E705 was found to form a group of H-bond interactions with D554/K588/K645 below the hydrophobic gate to stabilize the closed conformation of the pore in the Ca2+-free state. Interestingly, in the Ca2+ bound state, the E705 side chain swings 100o to serve as Ca2+-binding coordination and released K645. K645 is closer to the hydrophobic gate in the calcium-bound state, which facilitates the provision of electrostatic forces for chloride ions as the ions pass through the hydrophobic gate. Our findings provide the structural-based insights to understanding the mechanisms of gating of TMEM16A.
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Affiliation(s)
- Sai Shi
- State Key Laboratory of Reliability and Intelligence of Electrical Equipment, Hebei University of Technology, Tianjin 300401, China; Key Laboratory of Electromagnetic Field and Electrical Apparatus Reliability of Hebei Province, Hebei University of Technology, Tianjin 300401, China; Key Laboratory of Molecular Biophysics of Hebei Province, Institute of Biophysics, School of Science, Hebei University of Technology, Tianjin 300401, China
| | - Chunli Pang
- Key Laboratory of Molecular Biophysics of Hebei Province, Institute of Biophysics, School of Science, Hebei University of Technology, Tianjin 300401, China
| | - Shuxi Ren
- Key Laboratory of Molecular Biophysics of Hebei Province, Institute of Biophysics, School of Science, Hebei University of Technology, Tianjin 300401, China
| | - Fude Sun
- Key Laboratory of Molecular Biophysics of Hebei Province, Institute of Biophysics, School of Science, Hebei University of Technology, Tianjin 300401, China
| | - Biao Ma
- State Key Laboratory of Reliability and Intelligence of Electrical Equipment, Hebei University of Technology, Tianjin 300401, China; Key Laboratory of Electromagnetic Field and Electrical Apparatus Reliability of Hebei Province, Hebei University of Technology, Tianjin 300401, China; Key Laboratory of Molecular Biophysics of Hebei Province, Institute of Biophysics, School of Science, Hebei University of Technology, Tianjin 300401, China
| | - Shuai Guo
- College of Life Science, Hebei University, Baoding 071002, Hebei, China
| | - Junwei Li
- Key Laboratory of Molecular Biophysics of Hebei Province, Institute of Biophysics, School of Science, Hebei University of Technology, Tianjin 300401, China
| | - Yafei Chen
- Key Laboratory of Molecular Biophysics of Hebei Province, Institute of Biophysics, School of Science, Hebei University of Technology, Tianjin 300401, China
| | - Hailong An
- State Key Laboratory of Reliability and Intelligence of Electrical Equipment, Hebei University of Technology, Tianjin 300401, China; Key Laboratory of Electromagnetic Field and Electrical Apparatus Reliability of Hebei Province, Hebei University of Technology, Tianjin 300401, China; Key Laboratory of Molecular Biophysics of Hebei Province, Institute of Biophysics, School of Science, Hebei University of Technology, Tianjin 300401, China.
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Bengtsson RJ, Simpkin AJ, Pulford CV, Low R, Rasko DA, Rigden DJ, Hall N, Barry EM, Tennant SM, Baker KS. Pathogenomic analyses of Shigella isolates inform factors limiting shigellosis prevention and control across LMICs. Nat Microbiol 2022; 7:251-261. [PMID: 35102306 PMCID: PMC8813619 DOI: 10.1038/s41564-021-01054-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 12/17/2021] [Indexed: 12/17/2022]
Abstract
Shigella spp. are the leading bacterial cause of severe childhood diarrhoea in low- and middle-income countries (LMICs), are increasingly antimicrobial resistant and have no widely available licenced vaccine. We performed genomic analyses of 1,246 systematically collected shigellae sampled from seven countries in sub-Saharan Africa and South Asia as part of the Global Enteric Multicenter Study (GEMS) between 2007 and 2011, to inform control and identify factors that could limit the effectiveness of current approaches. Through contemporaneous comparison among major subgroups, we found that S. sonnei contributes ≥6-fold more disease than other Shigella species relative to its genomic diversity, and highlight existing diversity and adaptative capacity among S. flexneri that may generate vaccine escape variants in <6 months. Furthermore, we show convergent evolution of resistance against ciprofloxacin, the current WHO-recommended antimicrobial for the treatment of shigellosis, among Shigella isolates. This demonstrates the urgent need to integrate existing genomic diversity into vaccine and treatment plans for Shigella, providing a framework for the focused application of comparative genomics to guide vaccine development, and the optimization of control and prevention strategies for other pathogens relevant to public health policy considerations.
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Affiliation(s)
- Rebecca J Bengtsson
- Clinical Infection, Microbiology and Immunity, Institute of Infection, Veterinary and Ecological Sciences, The University of Liverpool, Liverpool, UK
| | - Adam J Simpkin
- Biochemistry and Systems Biology, Institute of Systems, Molecular and Systems Biology, The University of Liverpool, Liverpool, UK
| | - Caisey V Pulford
- Clinical Infection, Microbiology and Immunity, Institute of Infection, Veterinary and Ecological Sciences, The University of Liverpool, Liverpool, UK
- Gastrointestinal Infections and Food Safety (One Health), United Kingdom Health Security Agency, London, UK
| | - Ross Low
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - David A Rasko
- Department of Microbiology and Immunology, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Daniel J Rigden
- Biochemistry and Systems Biology, Institute of Systems, Molecular and Systems Biology, The University of Liverpool, Liverpool, UK
| | - Neil Hall
- Earlham Institute, Norwich Research Park, Norwich, UK
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Eileen M Barry
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Sharon M Tennant
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Kate S Baker
- Clinical Infection, Microbiology and Immunity, Institute of Infection, Veterinary and Ecological Sciences, The University of Liverpool, Liverpool, UK.
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48
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Felsztyna I, Villarreal MA, García DA, Miguel V. Insect RDL Receptor Models for Virtual Screening: Impact of the Template Conformational State in Pentameric Ligand-Gated Ion Channels. ACS OMEGA 2022; 7:1988-2001. [PMID: 35071887 PMCID: PMC8771969 DOI: 10.1021/acsomega.1c05465] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 12/28/2021] [Indexed: 06/14/2023]
Abstract
The RDL receptor is one of the most relevant protein targets for insecticide molecules. It belongs to the pentameric ligand-gated ion channel (pLGIC) family. Given that the experimental structures of pLGICs are difficult to obtain, homology modeling has been extensively used for these proteins, particularly for the RDL receptor. However, no detailed assessments of the usefulness of homology models for virtual screening (VS) have been carried out for pLGICs. The aim of this study was to evaluate which are the determinant factors for a good VS performance using RDL homology models, specially analyzing the impact of the template conformational state. Fifteen RDL homology models were obtained based on different pLGIC templates representing the closed, open, and desensitized states. A retrospective VS process was performed on each model, and their performance in the prioritization of active ligands was assessed. In addition, the three best-performing models among each of the conformations were subjected to molecular dynamics simulations (MDS) in complex with a representative active ligand. The models showed variations in their VS performance parameters that were related to the structural properties of the binding site. VS performance tended to improve in more constricted binding cavities. The best performance was obtained with a model based on a template in the closed conformation. MDS confirmed that the closed model was the one that best represented the interactions with an active ligand. These results imply that different templates should be evaluated and the structural variations between their channel conformational states should be specially examined, providing guidelines for the application of homology modeling for VS in other proteins of the pLGIC family.
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Affiliation(s)
- Iván Felsztyna
- Facultad
de Ciencias Exactas, Físicas y Naturales, Departamento de Química.
Cátedra de Química Biológica, Universidad Nacional de Córdoba, Córdoba 5016, Argentina
- Instituto
de Investigaciones Biológicas y Tecnológicas (IIByT), CONICET-Universidad Nacional de Córdoba, Córdoba 5016, Argentina
| | - Marcos A. Villarreal
- Facultad
de Ciencias Químicas, Departamento de Química Teórica
y Computacional, Universidad Nacional de
Córdoba, Córdoba 5016, Argentina
- Instituto
de Investigaciones en Físico-Química de Córdoba
(INFIQC), CONICET-Universidad Nacional de
Córdoba, Córdoba 5016, Argentina
| | - Daniel A. García
- Facultad
de Ciencias Exactas, Físicas y Naturales, Departamento de Química.
Cátedra de Química Biológica, Universidad Nacional de Córdoba, Córdoba 5016, Argentina
- Instituto
de Investigaciones Biológicas y Tecnológicas (IIByT), CONICET-Universidad Nacional de Córdoba, Córdoba 5016, Argentina
| | - Virginia Miguel
- Facultad
de Ciencias Exactas, Físicas y Naturales, Departamento de Química.
Cátedra de Química Biológica, Universidad Nacional de Córdoba, Córdoba 5016, Argentina
- Instituto
de Investigaciones Biológicas y Tecnológicas (IIByT), CONICET-Universidad Nacional de Córdoba, Córdoba 5016, Argentina
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49
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Topin J, Bouysset C, Pacalon J, Kim Y, Rhyu MR, Fiorucci S, Golebiowski J. Functional molecular switches of mammalian G protein-coupled bitter-taste receptors. Cell Mol Life Sci 2021; 78:7605-7615. [PMID: 34687318 PMCID: PMC11073308 DOI: 10.1007/s00018-021-03968-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 09/20/2021] [Accepted: 09/26/2021] [Indexed: 10/20/2022]
Abstract
Bitter taste receptors (TAS2Rs) are a poorly understood subgroup of G protein-coupled receptors (GPCRs). The experimental structure of these receptors has yet to be determined, and key-residues controlling their function remain mostly unknown. We designed an integrative approach to improve comparative modeling of TAS2Rs. Using current knowledge on class A GPCRs and existing experimental data in the literature as constraints, we pinpointed conserved motifs to entirely re-align the amino-acid sequences of TAS2Rs. We constructed accurate homology models of human TAS2Rs. As a test case, we examined the accuracy of the TAS2R16 model with site-directed mutagenesis and in vitro functional assays. This combination of in silico and in vitro results clarifies sequence-function relationships and proposes functional molecular switches that encode agonist sensing and downstream signaling mechanisms within mammalian TAS2Rs sequences.
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Affiliation(s)
- Jérémie Topin
- Institut de Chimie de Nice UMR7272, Université Côte d'Azur, CNRS, Nice, France.
| | - Cédric Bouysset
- Institut de Chimie de Nice UMR7272, Université Côte d'Azur, CNRS, Nice, France
| | - Jody Pacalon
- Institut de Chimie de Nice UMR7272, Université Côte d'Azur, CNRS, Nice, France
| | - Yiseul Kim
- Korea Food Research Institute, 245 Iseo-myeon, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - Mee-Ra Rhyu
- Korea Food Research Institute, 245 Iseo-myeon, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - Sébastien Fiorucci
- Institut de Chimie de Nice UMR7272, Université Côte d'Azur, CNRS, Nice, France.
| | - Jérôme Golebiowski
- Institut de Chimie de Nice UMR7272, Université Côte d'Azur, CNRS, Nice, France
- Department of Brain and Cognitive Sciences, DGIST, 333, Techno JungAng, Daero, HyeongPoong Myeon, Daegu, 711-873, Republic of Korea
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50
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Soto-Ospina A, Araque Marín P, Bedoya GDJ, Villegas Lanau A. Structural Predictive Model of Presenilin-2 Protein and Analysis of Structural Effects of Familial Alzheimer's Disease Mutations. Biochem Res Int 2021; 2021:9542038. [PMID: 34881055 PMCID: PMC8648483 DOI: 10.1155/2021/9542038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 10/21/2021] [Indexed: 12/12/2022] Open
Abstract
Alzheimer's disease manifests itself in brain tissue by neuronal death, due to aggregation of β-amyloid, produced by senile plaques, and hyperphosphorylation of the tau protein, which produces neurofibrillary tangles. One of the genetic markers of the disease is the gene that translates the presenilin-2 protein, which has mutations that favor the appearance of the disease and has no reported crystallographic structure. In view of this, protein modeling is performed using prediction and structural refinement tools followed by an energetic and stereochemical characterization for its validation. For the simulation, four reported mutations are chosen, which are Met239Ile, Met239Val, Ser130Leu, and Thr122Arg, all associated with various functional responses. From a theoretical analysis, a preliminary bioinformatic study is made to find the phosphorylation patterns in the protein and the hydropathic index according to the polarity and chemical environment. Molecular visualization was carried out with the Chimera 1.14 software, and the theoretical calculation with the hybrid quantum mechanics/molecular mechanics system from the semi-empirical method, with Spartan18 software and an AustinModel1 basis. These relationships allow for studying the system from a structural approach with the determination of small distance changes, potential surfaces, electrostatic maps, and angle changes, which favor the comparison between wild-type and mutant systems. With the results obtained, it is expected to complement experimental data reported in the literature from models that would allow us to understand the effects of the selected mutations.
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Affiliation(s)
- Alejandro Soto-Ospina
- University of Antioquia, Faculty of Medicine, Group Molecular Genetics, Medellín, Colombia
- University of Antioquia, Faculty of Medicine, Group Neuroscience of Antioquia, Medellín, Colombia
| | - Pedronel Araque Marín
- EIA University, School of Life Sciences, Research and Innovation in Chemistry Formulations Group, Envigado, Colombia
| | | | - Andrés Villegas Lanau
- University of Antioquia, Faculty of Medicine, Group Molecular Genetics, Medellín, Colombia
- University of Antioquia, Faculty of Medicine, Group Neuroscience of Antioquia, Medellín, Colombia
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