1
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Yang M, Ren W, Jin Z, Xu E, Shen Y. Enhanced high-temperature energy storage performances in polymer dielectrics by synergistically optimizing band-gap and polarization of dipolar glass. Nat Commun 2024; 15:8647. [PMID: 39368966 DOI: 10.1038/s41467-024-52791-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Accepted: 09/21/2024] [Indexed: 10/07/2024] Open
Abstract
Polymer dielectrics play an irreplaceable role in electrostatic capacitors in modern electrical systems, and have been intensively studied with their polarization and breakdown strength (Eb) optimized for high discharged energy density (Ud) at elevated temperatures. Small molecules have been explored as fillers, yet they deteriorate thermal stability of matrix which limits their optimal loading to ~1 wt%. Herein, we develop a polymer blend dielectric consisting of common polyimide and a bifunctional dipolar glass polymer which are synthesized from two small molecule components with wide band-gap and large dipole moment. The bifunctional dipolar glass with large molecular weight not only maintains thermal stability of polymer blends even at a high loading of 10 wt%, but also induces substantial enhancement in polarization and Eb than any of individual components does, achieving an ultrahigh Ud of 8.34 J cm-3 (150 °C) and 6.21 J cm-3 (200 °C) with a charge-discharge efficiency of 90%.
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Affiliation(s)
- Minzheng Yang
- State Key Lab of New Ceramics and Fine Processing, School of Materials Science and Engineering, Tsinghua University, Beijing, China
| | - Weibin Ren
- State Key Lab of New Ceramics and Fine Processing, School of Materials Science and Engineering, Tsinghua University, Beijing, China.
| | - Zenghui Jin
- State Key Lab of New Ceramics and Fine Processing, School of Materials Science and Engineering, Tsinghua University, Beijing, China
| | - Erxiang Xu
- State Key Lab of New Ceramics and Fine Processing, School of Materials Science and Engineering, Tsinghua University, Beijing, China
| | - Yang Shen
- State Key Lab of New Ceramics and Fine Processing, School of Materials Science and Engineering, Tsinghua University, Beijing, China.
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2
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Phulera S, Dickson CJ, Schwalen CJ, Khoshouei M, Cassell SJ, Sun Y, Condos T, Whicher J, Weihofen WA. Scorpion α-toxin LqhαIT specifically interacts with a glycan at the pore domain of voltage-gated sodium channels. Structure 2024; 32:1611-1620.e4. [PMID: 39181123 DOI: 10.1016/j.str.2024.07.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 06/13/2024] [Accepted: 07/30/2024] [Indexed: 08/27/2024]
Abstract
Voltage-gated sodium (Nav) channels sense membrane potential and drive cellular electrical activity. The deathstalker scorpion α-toxin LqhαIT exerts a strong action potential prolonging effect on Nav channels. To elucidate the mechanism of action of LqhαIT, we determined a 3.9 Å cryoelectron microscopy (cryo-EM) structure of LqhαIT in complex with the Nav channel from Periplaneta americana (NavPas). We found that LqhαIT binds to voltage sensor domain 4 and traps it in an "S4 down" conformation. The functionally essential C-terminal epitope of LqhαIT forms an extensive interface with the glycan scaffold linked to Asn330 of NavPas that augments a small protein-protein interface between NavPas and LqhαIT. A combination of molecular dynamics simulations, structural comparisons, and prior mutagenesis experiments demonstrates the functional importance of this toxin-glycan interaction. These findings establish a structural basis for the specificity achieved by scorpion α-toxins and reveal the conserved glycan as an essential component of the toxin-binding epitope.
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Affiliation(s)
- Swastik Phulera
- Discovery Sciences, Novartis Biomedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Callum J Dickson
- Global Discovery Chemistry, Novartis Biomedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Christopher J Schwalen
- Global Discovery Chemistry, Novartis Biomedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Maryam Khoshouei
- Discovery Sciences, Novartis Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Samantha J Cassell
- Discovery Sciences, Novartis Biomedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Yishan Sun
- Neuroscience, Novartis Biomedical Research, 22 Windsor St, Cambridge, MA 02139, USA
| | - Tara Condos
- Discovery Sciences, Novartis Biomedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Jonathan Whicher
- Discovery Sciences, Novartis Biomedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA.
| | - Wilhelm A Weihofen
- Discovery Sciences, Novartis Biomedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA.
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3
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Navarro G, Gómez-Autet M, Morales P, Rebassa JB, Llinas Del Torrent C, Jagerovic N, Pardo L, Franco R. Homodimerization of CB 2 cannabinoid receptor triggered by a bivalent ligand enhances cellular signaling. Pharmacol Res 2024; 208:107363. [PMID: 39179054 DOI: 10.1016/j.phrs.2024.107363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 08/17/2024] [Accepted: 08/18/2024] [Indexed: 08/26/2024]
Abstract
G protein-coupled receptors (GPCRs) exist within a landscape of interconvertible conformational states and in dynamic equilibrium between monomers and higher-order oligomers, both influenced by ligand binding. Here, we show that a homobivalent ligand formed by equal chromenopyrazole moieties as pharmacophores, connected by 14 methylene units, can modulate the dynamics of the cannabinoid CB2 receptor (CB2R) homodimerization by simultaneously binding both protomers of the CB2R-CB2R homodimer. Computational and pharmacological experiments showed that one of the ligand pharmacophores binds to the orthosteric site of one protomer, and the other pharmacophore to a membrane-oriented pocket between transmembranes 1 and 7 of the partner protomer. This results in unique pharmacological properties, including increased potency in Gi-mediated signaling and enhanced recruitment of β-arrestin. Thus, by modulating dimerization dynamics, it may be possible to fine-tune CB2R activity, potentially leading to improved therapeutic outcomes.
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Affiliation(s)
- Gemma Navarro
- Department of Biochemistry and Physiology. Faculty of Pharmacy and Food Sciences. Universitat de Barcelona, Barcelona 08028, Spain; Institute of Neuroscience, University of Barcelona (NeuroUB), Barcelona 08035, Spain; Centro de Investigación en Red, Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid 28031, Spain
| | - Marc Gómez-Autet
- Laboratory of Computational Medicine, Biostatistics Unit, Faculty of Medicine, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Paula Morales
- Medicinal Chemistry Institute, Spanish National Research Council, CSIC, Madrid 28006, Spain
| | - Joan Biel Rebassa
- Department of Biochemistry and Physiology. Faculty of Pharmacy and Food Sciences. Universitat de Barcelona, Barcelona 08028, Spain; Institute of Neuroscience, University of Barcelona (NeuroUB), Barcelona 08035, Spain
| | - Claudia Llinas Del Torrent
- Laboratory of Computational Medicine, Biostatistics Unit, Faculty of Medicine, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Nadine Jagerovic
- Medicinal Chemistry Institute, Spanish National Research Council, CSIC, Madrid 28006, Spain.
| | - Leonardo Pardo
- Laboratory of Computational Medicine, Biostatistics Unit, Faculty of Medicine, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain.
| | - Rafael Franco
- Centro de Investigación en Red, Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid 28031, Spain; Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, Barcelona 08028, Spain.
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4
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Zhang N, Dhumal D, Kuo SH, Lew SQ, Patil PD, Taher R, Vaidya S, Galanakou C, Elkihel A, Oh MW, Chong SY, Marson D, Zheng J, Rouvinski O, Abolarin WO, Pricl S, Lau GW, Lee LTO, Peng L. Targeting the phosphatidylglycerol lipid: An amphiphilic dendrimer as a promising antibacterial candidate. SCIENCE ADVANCES 2024; 10:eadn8117. [PMID: 39321303 PMCID: PMC11423894 DOI: 10.1126/sciadv.adn8117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 08/19/2024] [Indexed: 09/27/2024]
Abstract
The rapid emergence and spread of multidrug-resistant bacterial pathogens require the development of antibacterial agents that are robustly effective while inducing no toxicity or resistance development. In this context, we designed and synthesized amphiphilic dendrimers as antibacterial candidates. We report the promising potent antibacterial activity shown by the amphiphilic dendrimer AD1b, composed of a long hydrophobic alkyl chain and a tertiary amine-terminated poly(amidoamine) dendron, against a panel of Gram-negative bacteria, including multidrug-resistant Escherichia coli and Acinetobacter baumannii. AD1b exhibited effective activity against drug-resistant bacterial infections in vivo. Mechanistic studies revealed that AD1b targeted the membrane phospholipids phosphatidylglycerol (PG) and cardiolipin (CL), leading to the disruption of the bacterial membrane and proton motive force, metabolic disturbance, leakage of cellular components, and, ultimately, cell death. Together, AD1b that specifically interacts with PG/CL in bacterial membranes supports the use of small amphiphilic dendrimers as a promising strategy to target drug-resistant bacterial pathogens and addresses the global antibiotic crisis.
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Affiliation(s)
- Nian Zhang
- Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Dinesh Dhumal
- Aix-Marseille Universite, CNRS, Centre Interdisciplinaire de Nanoscience de Marseille, UMR 7325, "Equipe Labellisee Ligue Contre le Cancer," 13288 Marseille, France
| | - Shanny Hsuan Kuo
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Shi Qian Lew
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Pankaj D Patil
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA
| | - Raleb Taher
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA
| | - Sanika Vaidya
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA
| | - Christina Galanakou
- Aix-Marseille Universite, CNRS, Centre Interdisciplinaire de Nanoscience de Marseille, UMR 7325, "Equipe Labellisee Ligue Contre le Cancer," 13288 Marseille, France
| | - Abdechakour Elkihel
- Aix-Marseille Universite, CNRS, Centre Interdisciplinaire de Nanoscience de Marseille, UMR 7325, "Equipe Labellisee Ligue Contre le Cancer," 13288 Marseille, France
| | - Myung Whan Oh
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Sook Yin Chong
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Domenico Marson
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTS), DEA, University of Trieste, Trieste, Italy
| | - Jun Zheng
- Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Oleg Rouvinski
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA
| | - Williams O Abolarin
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA
| | - Sabrina Pricl
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTS), DEA, University of Trieste, Trieste, Italy
- Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Gee W Lau
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Leo Tsz On Lee
- Faculty of Health Sciences, University of Macau, Taipa, Macau, China
- Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa, Macau, China
- Ministry of Education Frontiers Science Center for Precision Oncology, University of Macau, Taipa, Macau, China
| | - Ling Peng
- Aix-Marseille Universite, CNRS, Centre Interdisciplinaire de Nanoscience de Marseille, UMR 7325, "Equipe Labellisee Ligue Contre le Cancer," 13288 Marseille, France
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5
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Liu S, Hao X, Miao D, Zhang Y. A Study on the Binding Mechanism and the Impact of Key Residue Mutations between SND1 and MTDH Peptide through Molecular Dynamics Simulations. J Phys Chem B 2024; 128:9074-9085. [PMID: 39276108 DOI: 10.1021/acs.jpcb.4c02325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/16/2024]
Abstract
Metastasis of breast cancer is the main cause of death for patients with breast cancer. The interaction between metadherin (MTDH) and staphylococcal nuclease domain 1 (SND1) plays a pivotal role in promoting breast cancer development. However, the binding details between MTDH and SND1 remain unclear. In this study, we employed all-atom molecular dynamics simulations (MDs) and conducted binding energy calculations to investigate the binding details and the impact of key residue mutations on binding. The mutations in key residues have not significantly affected the overall stability of the structure and the fluctuation of residues near the binding site; they have exerted a substantial impact on the binding of SND1 and MTDH peptide. The electrostatic interactions and van der Waals interactions play an important role in the binding of SND1 and the MTDH peptide. The mutations in the key residues have a significant impact on electrostatic and van der Waals interactions, resulting in weakened binding. The energy contributions of key residues mainly come from the electrostatic energy and van der Waals interactions of the side chain. In addition, the key residues form an intricate and stable network of hydrogen bonds and salt-bridge interactions with the MTDH peptide. The mutations in key residues have directly disrupt the interactions formed between SND1 and MTDH peptide, consequently leading to changes in the binding mode of the MTDH peptide. These analyses unveil the detailed atomic-level interaction mechanism between SND1 and the MTDH peptide, providing a molecular foundation for the development of antibreast cancer drugs.
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Affiliation(s)
- Senchen Liu
- School of Mathematics & Physics, Hebei University of Engineering, Handan 056038, China
| | - Xiafei Hao
- Medical College, Hebei University of Engineering, Handan 056038, China
| | - Dongqiang Miao
- School of Mathematics & Physics, Hebei University of Engineering, Handan 056038, China
| | - Yanjun Zhang
- School of Mathematics & Physics, Hebei University of Engineering, Handan 056038, China
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6
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Ślusarz MJ. Structural Basis for Antagonist Binding to Vasopressin V1b Receptor Revealed by the Molecular Dynamics Simulations. Biopolymers 2024:e23627. [PMID: 39286992 DOI: 10.1002/bip.23627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Revised: 08/24/2024] [Accepted: 08/30/2024] [Indexed: 09/19/2024]
Abstract
The human V1b receptor (V1bR) is primarily expressed in the corticotropic cells of the anterior pituitary where it is involved in the regulation of the hypothalamic-pituitary-adrenal (HPA) axis. The activation of V1bR induces the secretion of adrenocorticotropin hormone (ACTH) from the anterior pituitary cells which, in turn, stimulates the production of cortisol via the adrenal cortex. Clinical studies have demonstrated the chronic dysfunction of the HPA axis in patients with several psychiatric disorders. Thus, the inhibition of the V1b receptor and normalizing the HPA axis hyperactivity is a promising approach to the treatment of many stress-related disorders such as anxiety and depression. Nelivaptan is a selective V1bR antagonist that can be used for this purpose and an excellent molecule to study how antagonists interact with V1bR, especially since in recent years the experimental structures of vasopressin V2 and oxytocin receptors were solved, providing high-similarity templates for homology modeling of V1bR. Therefore, in this work, six independent molecular dynamics simulations of a V1bR-nelivaptan complex in a fully hydrated lipid bilayer, yielding a total simulation time of 6.0 μs, have been conducted. In the lowest-energy complexes obtained in this work and proposed to be the most probable structure of the V1bR-nelivaptan complex, the location of the ligand inside the receptor pocket is very similar to that of the other ligands observed in the experimental structures of the vasopressin/oxytocin receptor family. The receptor-ligand interaction has been analyzed and described, revealing the details of the molecular mechanism of this antagonist binding to V1bR and a probable contribution of L2005×40 and T2035×43 to binding selectivity.
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7
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Kim S. All-Atom Membrane Builder via Multiscale Simulation. J Chem Inf Model 2024. [PMID: 39250520 DOI: 10.1021/acs.jcim.4c01059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
I present an automated and flexible tool designed for constructing bilayer membranes at all-atom (AA) resolution. The builder initiates the construction and equilibration of bilayer membranes at Martini coarse-grained (CG) resolution, followed by resolution enhancement to the atomic level using the accompanying backmapping tool. Notably, this tool enables users to create bilayer membranes with user-defined lipid compositions and protein structures, while also offering the flexibility to accommodate new lipid types. To assess the simplicity and robustness of the tool, I demonstrate the construction of several membranes incorporating protein structures. The tool is freely available at github.com/ksy141/mstool.
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Affiliation(s)
- Siyoung Kim
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
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8
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Wang S, Wang K, Song K, Lai ZW, Li P, Li D, Sun Y, Mei Y, Xu C, Liao M. Structures of the Mycobacterium tuberculosis efflux pump EfpA reveal the mechanisms of transport and inhibition. Nat Commun 2024; 15:7710. [PMID: 39231991 PMCID: PMC11375168 DOI: 10.1038/s41467-024-51948-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 08/20/2024] [Indexed: 09/06/2024] Open
Abstract
As the first identified multidrug efflux pump in Mycobacterium tuberculosis (Mtb), EfpA is an essential protein and promising drug target. However, the functional and inhibitory mechanisms of EfpA are poorly understood. Here we report cryo-EM structures of EfpA in outward-open conformation, either bound to three endogenous lipids or the inhibitor BRD-8000.3. Three lipids inside EfpA span from the inner leaflet to the outer leaflet of the membrane. BRD-8000.3 occupies one lipid site at the level of inner membrane leaflet, competitively inhibiting lipid binding. EfpA resembles the related lysophospholipid transporter MFSD2A in both overall structure and lipid binding sites and may function as a lipid flippase. Combining AlphaFold-predicted EfpA structure, which is inward-open, we propose a complete conformational transition cycle for EfpA. Together, our results provide a structural and mechanistic foundation to comprehend EfpA function and develop EfpA-targeting anti-TB drugs.
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Affiliation(s)
- Shuhui Wang
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, USA.
| | - Kun Wang
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Kangkang Song
- Department of Biochemistry & Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Cryo-EM Core Facility, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Zon Weng Lai
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- mRNA Center of Excellence, Sanofi, Waltham, USA
| | - Pengfei Li
- Single Particle, LLC, San Diego, CA, USA
| | - Dongying Li
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Cryo-electron microscopy center, Southern University of Science and Technology, Shenzhen, China
| | - Yajie Sun
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ye Mei
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai, China
| | - Chen Xu
- Department of Biochemistry & Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Cryo-EM Core Facility, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Maofu Liao
- Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.
- Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, China.
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9
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Becker D, Bharatam PV, Gohlke H. Molecular Mechanisms Underlying Single Nucleotide Polymorphism-Induced Reactivity Decrease in CYP2D6. J Chem Inf Model 2024; 64:6026-6040. [PMID: 38994927 DOI: 10.1021/acs.jcim.4c00276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
Cytochrome P450 2D6 (CYP2D6) is one of the most important enzymes involved in drug metabolism. Genetic polymorphism can influence drug metabolism by CYP2D6 such that a therapy is seriously affected by under- or overdosing of drugs. However, a general explanation at the atomistic level for poor activity is missing so far. Here we show for the 20 most common single nucleotide polymorphisms (SNPs) of CYP2D6 that poor metabolism is driven by four mechanisms. We found in extensive all-atom molecular dynamics simulations that the rigidity of the I-helix (central helix), distance between central phenylalanines (stabilizing bound substrate), availability of basic residues on the surface of CYP2D6 (binding of cytochrome P450 reductase), and position of arginine 132 (electron transfer to heme) are essential for an extensive function of the enzyme. These results were applied to SNPs with unknown effects, and potential SNPs that may lead to poor drug metabolism were identified. The revealed molecular mechanisms might be important for other drug-metabolizing cytochrome P450 enzymes.
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Affiliation(s)
- Daniel Becker
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Prasad V Bharatam
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S. A. S. Nagar, Mohali, Punjab 160 062, India
| | - Holger Gohlke
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
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10
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Drosou M, Bhattacharjee S, Pantazis DA. Combined Multireference-Multiscale Approach to the Description of Photosynthetic Reaction Centers. J Chem Theory Comput 2024; 20. [PMID: 39116215 PMCID: PMC11360140 DOI: 10.1021/acs.jctc.4c00578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 07/02/2024] [Accepted: 07/12/2024] [Indexed: 08/10/2024]
Abstract
A first-principles description of the primary photochemical processes that drive photosynthesis and sustain life on our planet remains one of the grand challenges of modern science. Recent research established that explicit incorporation of protein electrostatics in excited-state calculations of photosynthetic pigments, achieved for example with quantum-mechanics/molecular-mechanics (QM/MM) approaches, is essential for a meaningful description of the properties and function of pigment-protein complexes. Although time-dependent density functional theory has been used productively so far in QM/MM approaches for the study of such systems, this methodology has limitations. Here we pursue for the first time a QM/MM description of the reaction center in the principal enzyme of oxygenic photosynthesis, Photosystem II, using multireference wave function theory for the high-level QM region. We identify best practices and establish guidelines regarding the rational choice of active space and appropriate state-averaging for the efficient and reliable use of complete active space self-consistent field (CASSCF) and the N-electron valence state perturbation theory (NEVPT2) in the prediction of low-lying excited states of chlorophyll and pheophytin pigments. Given that the Gouterman orbitals are inadequate as a minimal active space, we define specific minimal and extended active spaces for the NEVPT2 description of electronic states that fall within the Q and B bands. Subsequently, we apply our multireference-QM/MM protocol to the description of all pigments in the reaction center of Photosystem II. The calculations reproduce the electrochromic shifts induced by the protein matrix and the ordering of site energies consistent with the identity of the primary donor (ChlD1) and the experimentally known asymmetric and directional electron transfer. The optimized protocol sets the stage for future multireference treatments of multiple pigments, and hence for multireference studies of charge separation, while it is transferable to the study of any photoactive embedded tetrapyrrole system.
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Affiliation(s)
- Maria Drosou
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Sinjini Bhattacharjee
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Dimitrios A. Pantazis
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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11
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Llinas Del Torrent C, Raïch I, Gonzalez A, Lillo J, Casajuana-Martin N, Franco R, Pardo L, Navarro G. Allosterism in the adenosine A 2A and cannabinoid CB 2 heteromer. Br J Pharmacol 2024. [PMID: 39044481 DOI: 10.1111/bph.16502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 01/24/2024] [Accepted: 03/18/2024] [Indexed: 07/25/2024] Open
Abstract
BACKGROUND AND PURPOSE Allosterism is a regulatory mechanism for GPCRs that can be attained by ligand-binding or protein-protein interactions with another GPCR. We have studied the influence of the dimer interface on the allosteric properties of the A2A receptor and CB2 receptor heteromer. EXPERIMENTAL APPROACH We have evaluated cAMP production, phosphorylation of signal-regulated kinases (pERK1/2), label-free dynamic mass redistribution, β-arrestin 2 recruitment and bimolecular fluorescence complementation assays in the absence and presence of synthetic peptides that disrupt the formation of the heteromer. Molecular dynamic simulations provided converging evidence that the heteromeric interface influences the allosteric properties of the A2AR-CB2R heteromer. KEY RESULTS Apo A2AR blocks agonist-induced signalling of CB2R. The disruptive peptides, with the amino acid sequence of transmembrane (TM) 6 of A2AR or CB2R, facilitate CB2R activation, suggesting that A2AR allosterically prevents the outward movement of TM 6 of CB2R for G protein binding. Significantly, binding of the selective antagonist SCH 58261 to A2AR also facilitated agonist-induced activation of CB2R. CONCLUSIONS AND IMPLICATIONS It is proposed that the A2AR-CB2R heteromer contains distinct dimerization interfaces that govern its functional properties. The molecular interface between protomers of the A2AR-CB2R heteromer interconverted from TM 6 for apo or agonist-bound A2AR, blocking CB2R activation, to mainly the TM 1/7 interface for antagonist-bound A2AR, facilitating the independent opening of intracellular cavities for G protein binding. These novel results shed light on a different type of allosteric mechanism and extend the repertoire of GPCR heteromer signalling.
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Affiliation(s)
- Claudia Llinas Del Torrent
- Laboratory of Computational Medicine, Biostatistics Unit, Faculty of Medicine, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Iu Raïch
- Department of Biochemistry and Physiology, Faculty of Pharmacy and Food Sciences, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación en Red, Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
- Institute of Neuroscience, University of Barcelona (NeuroUB), Barcelona, Spain
| | - Angel Gonzalez
- Laboratory of Computational Medicine, Biostatistics Unit, Faculty of Medicine, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Jaume Lillo
- Centro de Investigación en Red, Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, Barcelona, Spain
| | - Nil Casajuana-Martin
- Laboratory of Computational Medicine, Biostatistics Unit, Faculty of Medicine, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Rafael Franco
- Centro de Investigación en Red, Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, Barcelona, Spain
| | - Leonardo Pardo
- Laboratory of Computational Medicine, Biostatistics Unit, Faculty of Medicine, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Gemma Navarro
- Department of Biochemistry and Physiology, Faculty of Pharmacy and Food Sciences, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación en Red, Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
- Institute of Neuroscience, University of Barcelona (NeuroUB), Barcelona, Spain
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12
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Pang P, Liu S, Hao X, Tian Y, Gong S, Miao D, Zhang Y. Exploring binding modes of the selected inhibitors to SND1 by all-atom molecular dynamics simulations. J Biomol Struct Dyn 2024; 42:5536-5550. [PMID: 37345536 DOI: 10.1080/07391102.2023.2226737] [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: 03/31/2023] [Accepted: 06/13/2023] [Indexed: 06/23/2023]
Abstract
Breast cancer is the leading cause of cancer-related deaths in women. Previous studies have indicated that disrupting the interaction between Metadherin (MTDH) and Staphylococcal nuclease domain containing 1 (SND1) can inhibit breast cancer development. Understanding the binding mode of small molecule inhibitors with SND1 is of great significance for designing drugs targeting the MTDH-SND1 complex. In this study, we conducted all-atom molecular dynamics (MD) simulations in solution and performed binding energy calculations to gain insights into the binding mechanism of small molecules to SND1. The binding site of SND1 for small molecules is relatively rigid, and the binding of the small molecule and the mutation of key residues have little effect on the conformation of the binding site. SND1 binds more tightly to C26-A6 than to C26-A2, as C26-A2 undergoes a 180° directional change during the simulation process. The key residue mutations have a direct effect on the position and orientation of small molecule in the binding site. The key residues make primary contributions to the binding energy through van der Waals interaction and nonpolar solvation energy, although the contribution from nonpolar solvation is relatively minor. The key residue mutations also affect the formation of hydrogen bonds and ultimately the stability of the small molecule-SND1 complex.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Peilin Pang
- School of Mathematics and Physics, Hebei University of Engineering, Handan, China
| | - Senchen Liu
- School of Mathematics and Physics, Hebei University of Engineering, Handan, China
| | - Xiafei Hao
- Medical College, Hebei University of Engineering, Handan, China
| | - Yuxin Tian
- School of Mathematics and Physics, Hebei University of Engineering, Handan, China
| | - Shuyue Gong
- School of Mathematics and Physics, Hebei University of Engineering, Handan, China
| | - Dongqiang Miao
- School of Mathematics and Physics, Hebei University of Engineering, Handan, China
| | - Yanjun Zhang
- School of Mathematics and Physics, Hebei University of Engineering, Handan, China
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13
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Kaiser J, Gertzen CGW, Bernauer T, Nitsche V, Höfner G, Niessen KV, Seeger T, Paintner FF, Wanner KT, Steinritz D, Worek F, Gohlke H. Identification of ligands binding to MB327-PAM-1, a binding pocket relevant for resensitization of nAChRs. Toxicol Lett 2024; 398:91-104. [PMID: 38768836 DOI: 10.1016/j.toxlet.2024.05.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 04/13/2024] [Accepted: 05/17/2024] [Indexed: 05/22/2024]
Abstract
Desensitization of nicotinic acetylcholine receptors (nAChRs) can be induced by overstimulation with acetylcholine (ACh) caused by an insufficient degradation of ACh after poisoning with organophosphorus compounds (OPCs). Currently, there is no generally applicable treatment for OPC poisoning that directly targets the desensitized nAChR. The bispyridinium compound MB327, an allosteric modulator of nAChR, has been shown to act as a resensitizer of nAChRs, indicating that drugs binding directly to nAChRs can have beneficial effects after OPC poisoning. However, MB327 also acts as an inhibitor of nAChRs at higher concentrations and can thus not be used for OPC poisoning treatment. Consequently, novel, more potent resensitizers are required. To successfully design novel ligands, the knowledge of the binding site is of utmost importance. Recently, we performed in silico studies to identify a new potential binding site of MB327, MB327-PAM-1, for which a more affine ligand, UNC0646, has been described. In this work, we performed ligand-based screening approaches to identify novel analogs of UNC0646 to help further understand the structure-affinity relationship of this compound class. Furthermore, we used structure-based screenings and identified compounds representing four new chemotypes binding to MB327-PAM-1. One of these compounds, cycloguanil, is the active metabolite of the antimalaria drug proguanil and shows a higher affinity towards MB327-PAM-1 than MB327. Furthermore, cycloguanil can reestablish the muscle force in soman-inhibited rat muscles. These results can act as a starting point to develop more potent resensitizers of nAChR and to close the gap in the treatment after OPC poisoning.
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Affiliation(s)
- Jesko Kaiser
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Christoph G W Gertzen
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Tamara Bernauer
- Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Valentin Nitsche
- Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Georg Höfner
- Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Karin V Niessen
- Bundeswehr Institute of Pharmacology and Toxicology, Munich, Germany
| | - Thomas Seeger
- Bundeswehr Institute of Pharmacology and Toxicology, Munich, Germany
| | - Franz F Paintner
- Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Klaus T Wanner
- Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Dirk Steinritz
- Bundeswehr Institute of Pharmacology and Toxicology, Munich, Germany
| | - Franz Worek
- Bundeswehr Institute of Pharmacology and Toxicology, Munich, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany; Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich, Jülich, Germany.
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14
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Kern NR, Lee J, Choi YK, Im W. CHARMM-GUI Multicomponent Assembler for modeling and simulation of complex multicomponent systems. Nat Commun 2024; 15:5459. [PMID: 38937468 PMCID: PMC11211406 DOI: 10.1038/s41467-024-49700-4] [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: 09/13/2023] [Accepted: 06/17/2024] [Indexed: 06/29/2024] Open
Abstract
Atomic-scale molecular modeling and simulation are powerful tools for computational biology. However, constructing models with large, densely packed molecules, non-water solvents, or with combinations of multiple biomembranes, polymers, and nanomaterials remains challenging and requires significant time and expertise. Furthermore, existing tools do not support such assemblies under the periodic boundary conditions (PBC) necessary for molecular simulation. Here, we describe Multicomponent Assembler in CHARMM-GUI that automates complex molecular assembly and simulation input preparation under the PBC. In this work, we demonstrate its versatility by preparing 6 challenging systems with varying density of large components: (1) solvated proteins, (2) solvated proteins with a pre-equilibrated membrane, (3) solvated proteins with a sheet-like nanomaterial, (4) solvated proteins with a sheet-like polymer, (5) a mixed membrane-nanomaterial system, and (6) a sheet-like polymer with gaseous solvent. Multicomponent Assembler is expected to be a unique cyberinfrastructure to study complex interactions between small molecules, biomacromolecules, polymers, and nanomaterials.
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Affiliation(s)
- Nathan R Kern
- Department of Computer Science & Engineering, Lehigh University, Bethlehem, PA, USA
| | - Jumin Lee
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA
| | - Yeol Kyo Choi
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA
| | - Wonpil Im
- Department of Computer Science & Engineering, Lehigh University, Bethlehem, PA, USA.
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA.
- Department of Bioengineering, Lehigh University, Bethlehem, PA, USA.
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15
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Kaneko H, Korenaga R, Nakamura R, Kawai S, Ando T, Shiroishi M. Binding characteristics of the doxepin E/Z-isomers to the histamine H 1 receptor revealed by receptor-bound ligand analysis and molecular dynamics study. J Mol Recognit 2024:e3098. [PMID: 38924170 DOI: 10.1002/jmr.3098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/14/2024] [Accepted: 06/08/2024] [Indexed: 06/28/2024]
Abstract
Doxepin is an antihistamine and tricyclic antidepressant that binds to the histamine H1 receptor (H1R) with high affinity. Doxepin is an 85:15 mixture of the E- and Z-isomers. The Z-isomer is well known to be more effective than the E-isomer, whereas based on the crystal structure of the H1R/doxepin complex, the hydroxyl group of Thr1123.37 is close enough to form a hydrogen bond with the oxygen atom of the E-isomer. The detailed binding characteristics and reasons for the differences remain unclear. In this study, we analyzed doxepin isomers bound to the receptor following extraction from a purified H1R protein complexed with doxepin. The ratio of the E- and Z-isomers bound to wild-type (WT) H1R was 55:45, indicating that the Z-isomer was bound to WT H1R with an approximately 5.2-fold higher affinity than the E-isomer. For the T1123.37V mutant, the E/Z ratio was 89:11, indicating that both isomers have similar affinities. Free energy calculations using molecular dynamics (MD) simulations also reproduced the experimental results of the relative binding free energy differences between the isomers for WT and T1123.37V. Furthermore, MD simulations revealed that the hydroxyl group of T1123.37 did not form hydrogen bonds with the E-isomer, but with the adjacent residues in the binding pocket. Analysis of the receptor-bound doxepin and MD simulations suggested that the hydroxyl group of T1123.37 contributes to the formation of a chemical environment in the binding pocket, which is slightly more favorable for the Z-isomer without hydrogen bonding with doxepin.
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Affiliation(s)
- Hiroto Kaneko
- Department of Biological Science and Technology, Tokyo University of Science, Tokyo, Japan
| | - Ryunosuke Korenaga
- Department of Biological Science and Technology, Tokyo University of Science, Tokyo, Japan
| | - Ryota Nakamura
- Department of Applied Electronics, Tokyo University of Science, Tokyo, Japan
| | - Shinnosuke Kawai
- Department of Applied Electronics, Tokyo University of Science, Tokyo, Japan
| | - Tadashi Ando
- Department of Applied Electronics, Tokyo University of Science, Tokyo, Japan
- Research Institute for Science and Technology, Tokyo University of Science, Chiba, Japan
| | - Mitsunori Shiroishi
- Department of Biological Science and Technology, Tokyo University of Science, Tokyo, Japan
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16
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Bernauer T, Nitsche V, Kaiser J, Gertzen CGW, Höfner G, Niessen KV, Seeger T, Steinritz D, Worek F, Gohlke H, Wanner KT, Paintner FF. Synthesis and biological evaluation of novel MB327 analogs as resensitizers for desensitized nicotinic acetylcholine receptors after intoxication with nerve agents. Toxicol Lett 2024; 397:151-162. [PMID: 38759939 DOI: 10.1016/j.toxlet.2024.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 05/06/2024] [Accepted: 05/14/2024] [Indexed: 05/19/2024]
Abstract
Poisoning with organophosphorus compounds, which can lead to a cholinergic crisis due to the inhibition of acetylcholinesterase and the subsequent accumulation of acetylcholine (ACh) in the synaptic cleft, is a serious problem for which treatment options are currently insufficient. Our approach to broadening the therapeutic spectrum is to use agents that interact directly with desensitized nicotinic acetylcholine receptors (nAChRs) in order to induce functional recovery after ACh overstimulation. Although MB327, one of the most prominent compounds investigated in this context, has already shown positive properties in terms of muscle force recovery, this compound is not suitable for use as a therapeutic agent due to its insufficient potency. By means of in silico studies based on our recently presented allosteric binding pocket at the nAChR, i.e. the MB327-PAM-1 binding site, three promising MB327 analogs with a 4-aminopyridinium ion partial structure (PTM0056, PTM0062, and PTM0063) were identified. In this study, we present the synthesis and biological evaluation of a series of new analogs of the aforementioned compounds with a 4-aminopyridinium ion partial structure (PTM0064-PTM0072), as well as hydroxy-substituted analogs of MB327 (PTMD90-0012 and PTMD90-0015) designed to substitute entropically unfavorable water clusters identified during molecular dynamics simulations. The compounds were characterized in terms of their binding affinity towards the aforementioned binding site by applying the UNC0642 MS Binding Assays and in terms of their muscle force reactivation in rat diaphragm myography. More potent compounds were identified compared to MB327, as some of them showed a higher affinity towards MB327-PAM-1 and also a higher recovery of neuromuscular transmission at lower compound concentrations. To improve the treatment of organophosphate poisoning, direct targeting of nAChRs with appropriate compounds is a key step, and this study is an important contribution to this research.
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Affiliation(s)
- Tamara Bernauer
- Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Valentin Nitsche
- Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Jesko Kaiser
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Christoph G W Gertzen
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Georg Höfner
- Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Karin V Niessen
- Bundeswehr Institute of Pharmacology and Toxicology, Munich, Germany
| | - Thomas Seeger
- Bundeswehr Institute of Pharmacology and Toxicology, Munich, Germany
| | - Dirk Steinritz
- Bundeswehr Institute of Pharmacology and Toxicology, Munich, Germany
| | - Franz Worek
- Bundeswehr Institute of Pharmacology and Toxicology, Munich, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany; John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry) & Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich, Jülich, Germany
| | - Klaus T Wanner
- Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Franz F Paintner
- Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany.
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17
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Santana OL, Silva DG, Santana SR. Solvate Suite: A Command-Line Interface for Molecular Simulations and Multiscale Microsolvation Modeling. J Chem Inf Model 2024; 64:3767-3778. [PMID: 38621228 DOI: 10.1021/acs.jcim.3c01899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
In this work, we introduce the Solvate Suite, a comprehensive and modular command-line interface designed for molecular simulation and microsolvation modeling. The suite interfaces with widely used scientific software, streamlining computational experiments for liquid systems through the automated creation of simulation boxes and topology with adjustable simulation parameters. Furthermore, it has features for graphical and statistical analysis of simulated properties and extraction of trajectory configurations with various filters. Additionally, it introduces innovative strategies for microsolvation modeling with a multiscale approach, employing equilibrated dynamics to identify favorable solute-solvent interactions and enabling full cluster optimization for free-energy calculations without imaginary frequency contamination.
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Affiliation(s)
- Otávio L Santana
- Chemistry Department, Federal University of Paraíba, João Pessoa, Paraíba 58051-900, Brazil
| | - Daniel G Silva
- Chemistry Department, Federal University of Paraíba, João Pessoa, Paraíba 58051-900, Brazil
| | - Sidney R Santana
- Chemistry and Physics Department, Federal University of Paraíba, Areia, Paraíba 58397-000, Brazil
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18
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Ślusarz MJ, Lipińska AD. An intrinsic network of polar interactions is responsible for binding of UL49.5 C-degron by the CRL2 KLHDC3 ubiquitin ligase. Proteins 2024; 92:610-622. [PMID: 38069558 DOI: 10.1002/prot.26651] [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: 06/05/2023] [Revised: 11/14/2023] [Accepted: 11/27/2023] [Indexed: 04/13/2024]
Abstract
Bovine herpesvirus type 1 (BoHV-1) is a pathogen of cattle responsible for infectious bovine rhinotracheitis. The BoHV-1 UL49.5 is a transmembrane protein that binds to the transporter associated with antigen processing (TAP) and downregulates cell surface expression of the antigenic peptide complexes with the major histocompatibility complex class I (MHC-I). KLHDC3 is a kelch domain-containing protein 3 and a substrate receptor of a cullin2-RING (CRL2) E3 ubiquitin ligase. Recently, it has been identified that CRL2KLHDC3 is responsible for UL49.5-triggered TAP degradation via a C-degron pathway and the presence of the degron sequence does not lead to the degradation of UL49.5 itself. The molecular modeling of KLHDC3 in complexes with four UL49.5 C-terminal decapeptides (one native protein and three mutants) revealed their activity to be closely correlated with the conformation which they adopt in KLHDC3 binding cleft. To analyze the interaction between UL49.5 and KLHDC3 in detail, in this work a total of 3.6 μs long molecular dynamics simulations have been performed. The complete UL49.5-KLHDC3 complexes were embedded into the fully hydrated all-atom lipid membrane model with explicit water molecules. The network of polar interactions has been proposed to be responsible for the recognition and binding of the degron in KLHDC3. The interaction network within the binding pocket appeared to be very similar between two CRL2 substrate receptors: KLHDC3 and KLHDC2.
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Affiliation(s)
| | - Andrea D Lipińska
- Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland
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19
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Kawato S, Sato S, Kitoh-Nishioka H, Saga Y. Spectral changes of light-harvesting complex 2 lacking B800 bacteriochlorophyll a under neutral pH conditions. Photochem Photobiol Sci 2024; 23:871-879. [PMID: 38564166 DOI: 10.1007/s43630-024-00560-3] [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: 12/15/2023] [Accepted: 03/05/2024] [Indexed: 04/04/2024]
Abstract
Exchange of B800 bacteriochlorophyll (BChl) a in light-harvesting complex 2 (LH2) is promising for a better understanding of the mechanism on intracomplex excitation energy transfer of this protein. Structural and spectroscopic properties of LH2 lacking B800 BChl a (B800-depleted LH2), which is an important intermediate protein in the B800 exchange, will be useful to tackle the energy transfer mechanism in LH2 by the B800 exchange strategy. In this study, we report a unique spectral change of B800-depleted LH2, in which the Qy absorption band of B800 BChl a is automatically recovered under neutral pH conditions. This spectral change was facilitated by factors for destabilization of LH2, namely, a detergent, lauryl dimethylamine N-oxide, and an increase in temperature. Spectral analyses in the preparation of an LH2 variant denoted as B800-recovered LH2 indicated that most BChl a that was released by decomposition of part of B800-depleted LH2 was a source of the production of B800-recovered LH2. Characterization of purified B800-recovered LH2 demonstrated that its spectroscopic and structural features was quite similar to those of native LH2. The current results indicate that the recovery of the B800 Qy band of B800-depleted LH2 originates from the combination of decomposition of part of B800-depleted LH2 and in situ reconstitution of BChl a into the B800 binding pockets of residual B800-depleted LH2, resulting in the formation of stable B800-recovered LH2.
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Affiliation(s)
- Shota Kawato
- Faculty of Science and Engineering, Kindai University, Higashi-Osaka, Osaka, 577-8502, Japan
| | - Shinichi Sato
- Faculty of Science and Engineering, Kindai University, Higashi-Osaka, Osaka, 577-8502, Japan
| | - Hirotaka Kitoh-Nishioka
- Faculty of Science and Engineering, Kindai University, Higashi-Osaka, Osaka, 577-8502, Japan
| | - Yoshitaka Saga
- Faculty of Science and Engineering, Kindai University, Higashi-Osaka, Osaka, 577-8502, Japan.
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20
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Gentile R, Modric M, Thiele B, Jaeger KE, Kovacic F, Schott-Verdugo S, Gohlke H. Molecular Mechanisms Underlying Medium-Chain Free Fatty Acid-Regulated Activity of the Phospholipase PlaF from Pseudomonas aeruginosa. JACS AU 2024; 4:958-973. [PMID: 38559719 PMCID: PMC10976570 DOI: 10.1021/jacsau.3c00725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 04/04/2024]
Abstract
PlaF is a membrane-bound phospholipase A1 from Pseudomonas aeruginosa that is involved in remodeling membrane glycerophospholipids (GPLs) and modulating virulence-associated signaling and metabolic pathways. Previously, we identified the role of medium-chain free fatty acids (FFAs) in inhibiting PlaF activity and promoting homodimerization, yet the underlying molecular mechanism remained elusive. Here, we used unbiased and biased molecular dynamics simulations and free energy computations to assess how PlaF interacts with FFAs localized in the water milieu surrounding the bilayer or within the bilayer and how these interactions regulate PlaF activity. Medium-chain FFAs localized in the upper bilayer leaflet can stabilize inactive dimeric PlaF, likely through interactions with charged surface residues, as has been experimentally validated. Potential of mean force (PMF) computations indicate that membrane-bound FFAs may facilitate the activation of monomeric PlaF by lowering the activation barrier for changing into a tilted, active configuration. We estimated that the coupled equilibria of PlaF monomerization-dimerization and tilting at the physiological concentration of PlaF lead to the majority of PlaF forming inactive dimers when in a cell membrane loaded with decanoic acid (C10). This is in agreement with a suggested in vivo product feedback loop and gas chromatography-mass spectrometry profiling results, indicating that PlaF catalyzes the release of C10 from P. aeruginosa membranes. Additionally, we found that C10 in the water milieu can access the catalytic site of active monomeric PlaF, contributing to the competitive component of C10-mediated PlaF inhibition. Our study provides mechanistic insights into how medium-chain FFAs may regulate the activity of PlaF, a potential bacterial drug target.
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Affiliation(s)
- Rocco Gentile
- Institute
for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Matea Modric
- Institute
of Molecular Enzyme Technology, Heinrich
Heine University Düsseldorf, Forschungszentrum Jülich
GmbH, 52425 Jülich, Germany
| | - Björn Thiele
- Institute
of Bio- and Geosciences (IBG-2: Plant Sciences and IBG-3: Agrosphere), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Karl-Erich Jaeger
- Institute
of Molecular Enzyme Technology, Heinrich
Heine University Düsseldorf, Forschungszentrum Jülich
GmbH, 52425 Jülich, Germany
- Institute
of Bio- and Geosciences (IBG-1: Biotechnology), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Filip Kovacic
- Institute
of Molecular Enzyme Technology, Heinrich
Heine University Düsseldorf, Forschungszentrum Jülich
GmbH, 52425 Jülich, Germany
| | - Stephan Schott-Verdugo
- Institute
of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Holger Gohlke
- Institute
for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
- Institute
of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
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21
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Nguyen ATP, Weigle AT, Shukla D. Functional regulation of aquaporin dynamics by lipid bilayer composition. Nat Commun 2024; 15:1848. [PMID: 38418487 PMCID: PMC10901782 DOI: 10.1038/s41467-024-46027-y] [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: 07/21/2023] [Accepted: 02/12/2024] [Indexed: 03/01/2024] Open
Abstract
With the diversity of lipid-protein interactions, any observed membrane protein dynamics or functions directly depend on the lipid bilayer selection. However, the implications of lipid bilayer choice are seldom considered unless characteristic lipid-protein interactions have been previously reported. Using molecular dynamics simulation, we characterize the effects of membrane embedding on plant aquaporin SoPIP2;1, which has no reported high-affinity lipid interactions. The regulatory impacts of a realistic lipid bilayer, and nine different homogeneous bilayers, on varying SoPIP2;1 dynamics are examined. We demonstrate that SoPIP2;1's structure, thermodynamics, kinetics, and water transport are altered as a function of each membrane construct's ensemble properties. Notably, the realistic bilayer provides stabilization of non-functional SoPIP2;1 metastable states. Hydrophobic mismatch and lipid order parameter calculations further explain how lipid ensemble properties manipulate SoPIP2;1 behavior. Our results illustrate the importance of careful bilayer selection when studying membrane proteins. To this end, we advise cautionary measures when performing membrane protein molecular dynamics simulations.
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Affiliation(s)
- Anh T P Nguyen
- Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Austin T Weigle
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
- Department of Plant Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
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22
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Zhang Y, Miao D, Liu S, Hao X. Revealing the binding mechanism of BACE1 inhibitors through molecular dynamics simulations. J Biomol Struct Dyn 2024:1-13. [PMID: 38375603 DOI: 10.1080/07391102.2024.2319676] [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: 12/09/2023] [Accepted: 02/11/2024] [Indexed: 02/21/2024]
Abstract
Alzheimer's disease is a debilitating neurodegenerative disorder, and the Beta-Site Amyloid Precursor Protein Cleaving Enzyme 1 (BACE1) is a key therapeutic target in its treatment. This study employs molecular dynamics simulations and binding energy analysis to investigate the binding interactions between BACE1 and four selected small molecules: CNP520, D9W, NB641, and NB360. The binding model analysis indicates that the binding of BACE1 with four molecules are stable, except the loop regions show significant fluctuation. The binding free energy analyses reveal that NB360 exhibits the highest binding affinity with BACE1, surpassing other molecules (CNP520, D9W, and NB641). Detailed energy component assessments highlight the critical roles of electrostatic interactions and van der Waals forces in the binding process. Furthermore, residue contribution analysis identifies key amino acids influencing the binding process across all systems. Hydrogen bond analysis reveals a limited number of bonds between BACE1 and each small molecule, highlighting the importance of structural modifications to enable more stable hydrogen bonds. This research provides valuable insights into the molecular mechanisms of potential Alzheimer's disease therapeutics, guiding the way for improved drug design and the development of effective treatments targeting BACE1.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yanjun Zhang
- School of Mathematics & Physics, Hebei University of Engineering, Handan, China
| | - Dongqiang Miao
- School of Mathematics & Physics, Hebei University of Engineering, Handan, China
| | - Senchen Liu
- School of Mathematics & Physics, Hebei University of Engineering, Handan, China
| | - Xiafei Hao
- Medical College, Hebei University of Engineering, Handan, China
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23
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Vu NP, Ali L, Chua TL, Barr DA, Hendrickson HP, Trivedi DJ. Computational Insights into Prostaglandin E 2 Ligand Binding and Activation of G-Protein-Coupled Receptors. ACS APPLIED BIO MATERIALS 2024; 7:579-587. [PMID: 37058420 DOI: 10.1021/acsabm.2c01049] [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] [Indexed: 04/15/2023]
Abstract
G-protein coupled receptors (GPCRs) are eukaryotic integral membrane proteins that regulate signal transduction cascade pathways implicated in a variety of human diseases and are consequently of interest as drug targets. For this reason, it is of interest to investigate the way in which specific ligands bind and trigger conformational changes in the receptor during activation and how this in turn modulates intracellular signaling. In the present study, we investigate the way in which the ligand Prostaglandin E2 interacts with three GPCRs in the E-prostanoid family: EP1, EP2, and EP3. We examine information transfer pathways based on long-time scale molecular dynamics simulations using transfer entropy and betweenness centrality to measure the physical transfer of information among residues in the system. We monitor specific residues involved in binding to the ligand and investigate how the information transfer behavior of these residues changes upon ligand binding. Our results provide key insights that enable a deeper understanding of EP activation and signal transduction functioning pathways at the molecular level, as well as enabling us to make some predictions about the activation pathway for the EP1 receptor, for which little structural information is currently available. Our results should advance ongoing efforts in the development of potential therapeutics targeting these receptors.
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Affiliation(s)
- Nam P Vu
- Department of Chemistry, Lafayette College, Easton, Pennsylvania 18042, United States
| | - Luke Ali
- Department of Physics, Clarkson University, Potsdam, New York 13699, United States
| | - Theresa L Chua
- Department of Chemistry, Lafayette College, Easton, Pennsylvania 18042, United States
| | - Daniel A Barr
- Department of Chemistry, University of Mary, Bismarck, North Dakota 58504, United States
| | - Heidi P Hendrickson
- Department of Chemistry, Lafayette College, Easton, Pennsylvania 18042, United States
| | - Dhara J Trivedi
- Department of Physics, Clarkson University, Potsdam, New York 13699, United States
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24
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Mei Y, Shen Y. Cation-π Interactions Greatly Influence Ion Transportability of the Light-Driven Sodium Pump KR2: A Molecular Dynamics Study. J Chem Inf Model 2024; 64:974-982. [PMID: 38237560 DOI: 10.1021/acs.jcim.3c01883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2024]
Abstract
Krokinobacter eikastus rhodopsin 2 (KR2) is a typical light-driven sodium pump. Although wild-type KR2 exhibits high Na+ selectivity, mutagenesis performed on the residues constituting the entrance enables permeation of K+ and Cs+, while the underlying mechanism remains elusive. This study presents a comprehensive molecular dynamics investigation, including force field optimization, metadynamics, and alchemical free energy methods, to explore the N61L/G263F mutant of KR2, which exhibits transportability for K+ and Cs+. The introduced Phe263 residue can directly promote ion binding at the entrance through cation-π interactions, while the N61L mutation can enhance ion binding at Phe46 by relieving steric hindrance. These results suggest that cation-π interactions may significantly influence the ion transportability and selectivity of KR2, which can provide important insights for protein engineering and the design of artificial ion transporters.
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Affiliation(s)
- Yunhao Mei
- School of Chemistry, IGCME, Sun Yat-sen University, Guangzhou 510006, China
| | - Yong Shen
- School of Chemistry, IGCME, Sun Yat-sen University, Guangzhou 510006, China
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25
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Nitsche V, Höfner G, Kaiser J, Gertzen CGW, Seeger T, Niessen KV, Steinritz D, Worek F, Gohlke H, Paintner FF, Wanner KT. MS Binding Assays with UNC0642 as reporter ligand for the MB327 binding site of the nicotinic acetylcholine receptor. Toxicol Lett 2024; 392:94-106. [PMID: 38216073 DOI: 10.1016/j.toxlet.2024.01.003] [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: 11/19/2023] [Revised: 12/28/2023] [Accepted: 01/06/2024] [Indexed: 01/14/2024]
Abstract
Intoxications with organophosphorus compounds (OPCs) based chemical warfare agents and insecticides may result in a detrimental overstimulation of muscarinic and nicotinic acetylcholine receptors evolving into a cholinergic crisis leading to death due to respiratory failure. In the case of the nicotinic acetylcholine receptor (nAChR), overstimulation leads to a desensitization of the receptor, which cannot be pharmacologically treated so far. Still, compounds interacting with the MB327 binding site of the nAChR like the bispyridinium salt MB327 have been found to re-establish the functional activity of the desensitized receptor. Only recently, a series of quinazoline derivatives with UNC0642 as one of the most prominent representatives has been identified to address the MB327 binding site of the nAChR, as well. In this study, UNC0642 has been utilized as a reporter ligand to establish new Binding Assays for this target. These assays follow the concept of MS Binding Assays for which by assessing the amount of bound reporter ligand by mass spectrometry no radiolabeled material is required. According to the results of the performed MS Binding Assays comprising saturation and competition experiments it can be concluded, that UNC0642 used as a reporter ligand addresses the MB327 binding site of the Torpedo-nAChR. This is further supported by the outcome of ex vivo studies carried out with poisoned rat diaphragm muscles as well as by in silico studies predicting the binding mode of UNC0646, an analog of UNC0642 with the highest binding affinity, in the recently proposed binding site of MB327 (MB327-PAM-1). With UNC0642 addressing the MB327 binding site of the Torpedo-nAChR, this and related quinazoline derivatives represent a promising starting point for the development of novel ligands of the nAChR as antidotes for the treatment of intoxications with organophosphorus compounds. Further, the new MS Binding Assays are a potent alternative to established assays and of particular value, as they do not require the use of radiolabeled material and are based on a commercially available compound as reporter ligand, UNC0642, exhibiting one of the highest binding affinities for the MB327 binding site known so far.
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Affiliation(s)
- Valentin Nitsche
- Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Georg Höfner
- Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Jesko Kaiser
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine Universität Düsseldorf, Düsseldorf, Germany
| | - Christoph G W Gertzen
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine Universität Düsseldorf, Düsseldorf, Germany
| | - Thomas Seeger
- Bundeswehr Institute of Pharmacology and Toxicology, Munich, Germany
| | - Karin V Niessen
- Bundeswehr Institute of Pharmacology and Toxicology, Munich, Germany
| | - Dirk Steinritz
- Bundeswehr Institute of Pharmacology and Toxicology, Munich, Germany
| | - Franz Worek
- Bundeswehr Institute of Pharmacology and Toxicology, Munich, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine Universität Düsseldorf, Düsseldorf, Germany; Institute of Bio, and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich, Jülich, Germany
| | - Franz F Paintner
- Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Klaus T Wanner
- Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany.
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26
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Mills KR, Torabifard H. Computational approaches to investigate fluoride binding, selectivity and transport across the membrane. Methods Enzymol 2024; 696:109-154. [PMID: 38658077 DOI: 10.1016/bs.mie.2024.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The use of molecular dynamics (MD) simulations to study biomolecular systems has proven reliable in elucidating atomic-level details of structure and function. In this chapter, MD simulations were used to uncover new insights into two phylogenetically unrelated bacterial fluoride (F-) exporters: the CLCF F-/H+ antiporter and the Fluc F- channel. The CLCF antiporter, a member of the broader CLC family, has previously revealed unique stoichiometry, anion-coordinating residues, and the absence of an internal glutamate crucial for proton import in the CLCs. Through MD simulations enhanced with umbrella sampling, we provide insights into the energetics and mechanism of the CLCF transport process, including its selectivity for F- over HF. In contrast, the Fluc F- channel presents a novel architecture as a dual topology dimer, featuring two pores for F- export and a central non-transported sodium ion. Using computational electrophysiology, we simulate the electrochemical gradient necessary for F- export in Fluc and reveal details about the coordination and hydration of both F- and the central sodium ion. The procedures described here delineate the specifics of these advanced techniques and can also be adapted to investigate other membrane protein systems.
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Affiliation(s)
- Kira R Mills
- Department of Chemistry & Biochemistry, The University of Texas at Dallas, Richardson, TX, United States
| | - Hedieh Torabifard
- Department of Chemistry & Biochemistry, The University of Texas at Dallas, Richardson, TX, United States.
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27
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Ruiz Munevar M, Rizzi V, Portioli C, Vidossich P, Cao E, Parrinello M, Cancedda L, De Vivo M. Cation Chloride Cotransporter NKCC1 Operates through a Rocking-Bundle Mechanism. J Am Chem Soc 2024; 146:552-566. [PMID: 38146212 PMCID: PMC10786066 DOI: 10.1021/jacs.3c10258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 12/27/2023]
Abstract
The sodium, potassium, and chloride cotransporter 1 (NKCC1) plays a key role in tightly regulating ion shuttling across cell membranes. Lately, its aberrant expression and function have been linked to numerous neurological disorders and cancers, making it a novel and highly promising pharmacological target for therapeutic interventions. A better understanding of how NKCC1 dynamically operates would therefore have broad implications for ongoing efforts toward its exploitation as a therapeutic target through its modulation. Based on recent structural data on NKCC1, we reveal conformational motions that are key to its function. Using extensive deep-learning-guided atomistic simulations of NKCC1 models embedded into the membrane, we captured complex dynamical transitions between alternate open conformations of the inner and outer vestibules of the cotransporter and demonstrated that NKCC1 has water-permeable states. We found that these previously undefined conformational transitions occur via a rocking-bundle mechanism characterized by the cooperative angular motion of transmembrane helices (TM) 4 and 9, with the contribution of the extracellular tip of TM 10. We found these motions to be critical in modulating ion transportation and in regulating NKCC1's water transporting capabilities. Specifically, we identified interhelical dynamical contacts between TM 10 and TM 6, which we functionally validated through mutagenesis experiments of 4 new targeted NKCC1 mutants. We conclude showing that those 4 residues are highly conserved in most Na+-dependent cation chloride cotransporters (CCCs), which highlights their critical mechanistic implications, opening the way to new strategies for NKCC1's function modulation and thus to potential drug action on selected CCCs.
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Affiliation(s)
- Manuel
José Ruiz Munevar
- Laboratory
of Molecular Modelling & Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, Genoa 16163, Italy
| | - Valerio Rizzi
- Biomolecular
& Pharmaceutical Modelling Group, Université
de Genève, Rue Michel-Servet 1, Geneva CH-1211 4, Switzerland
| | - Corinne Portioli
- Laboratory
of Nanotechnology for Precision Medicine, Istituto Italiano di Tecnologia, Via Morego 30, Genoa 16163, Italy
- Laboratory
of Brain Development and Disease, Istituto
Italiano di Tecnologia, Via Morego 30, Genoa 16163, Italy
| | - Pietro Vidossich
- Laboratory
of Molecular Modelling & Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, Genoa 16163, Italy
| | - Erhu Cao
- Department
of Biochemistry, University of Utah School
of Medicine, Salt Lake City, Utah 84112-5650, United States
| | - Michele Parrinello
- Laboratory
of Atomistic Simulations, Istituto Italiano
di Tecnologia, Via Morego 30, Genoa 16163, Italy
| | - Laura Cancedda
- Laboratory
of Brain Development and Disease, Istituto
Italiano di Tecnologia, Via Morego 30, Genoa 16163, Italy
| | - Marco De Vivo
- Laboratory
of Molecular Modelling & Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, Genoa 16163, Italy
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28
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Kiani YS, Jabeen I. Challenges of Protein-Protein Docking of the Membrane Proteins. Methods Mol Biol 2024; 2780:203-255. [PMID: 38987471 DOI: 10.1007/978-1-0716-3985-6_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
Abstract
Despite the recent advances in the determination of high-resolution membrane protein (MP) structures, the structural and functional characterization of MPs remains extremely challenging, mainly due to the hydrophobic nature, low abundance, poor expression, purification, and crystallization difficulties associated with MPs. Whereby the major challenges/hurdles for MP structure determination are associated with the expression, purification, and crystallization procedures. Although there have been significant advances in the experimental determination of MP structures, only a limited number of MP structures (approximately less than 1% of all) are available in the Protein Data Bank (PDB). Therefore, the structures of a large number of MPs still remain unresolved, which leads to the availability of widely unplumbed structural and functional information related to MPs. As a result, recent developments in the drug discovery realm and the significant biological contemplation have led to the development of several novel, low-cost, and time-efficient computational methods that overcome the limitations of experimental approaches, supplement experiments, and provide alternatives for the characterization of MPs. Whereby the fine tuning and optimizations of these computational approaches remains an ongoing endeavor.Computational methods offer a potential way for the elucidation of structural features and the augmentation of currently available MP information. However, the use of computational modeling can be extremely challenging for MPs mainly due to insufficient knowledge of (or gaps in) atomic structures of MPs. Despite the availability of numerous in silico methods for 3D structure determination the applicability of these methods to MPs remains relatively low since all methods are not well-suited or adequate for MPs. However, sophisticated methods for MP structure predictions are constantly being developed and updated to integrate the modifications required for MPs. Currently, different computational methods for (1) MP structure prediction, (2) stability analysis of MPs through molecular dynamics simulations, (3) modeling of MP complexes through docking, (4) prediction of interactions between MPs, and (5) MP interactions with its soluble partner are extensively used. Towards this end, MP docking is widely used. It is notable that the MP docking methods yet few in number might show greater potential in terms of filling the knowledge gap. In this chapter, MP docking methods and associated challenges have been reviewed to improve the applicability, accuracy, and the ability to model macromolecular complexes.
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Affiliation(s)
- Yusra Sajid Kiani
- School of Interdisciplinary Engineering and Sciences (SINES), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Ishrat Jabeen
- School of Interdisciplinary Engineering and Sciences (SINES), National University of Sciences and Technology (NUST), Islamabad, Pakistan.
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29
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Vila-Julià G, Rubio-Martinez J, Perez JJ. Assessment of the bound conformation of bombesin to the BB1 and BB2 receptors. Int J Biol Macromol 2024; 255:127843. [PMID: 37956803 DOI: 10.1016/j.ijbiomac.2023.127843] [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: 10/31/2023] [Accepted: 10/31/2023] [Indexed: 11/15/2023]
Abstract
Bombesin is an endogenous peptide involved in a wide spectrum of physiological activities ranging from satiety, control of circadian rhythm and thermoregulation in the central nervous system, to stimulation of gastrointestinal hormone release, activation of macrophages and effects on development in peripheral tissues. Actions of the peptide are mediated through the two high affinity G-protein coupled receptors BB1R and BB2R. Under pathophysiological conditions, these receptors are overexpressed in many different types of tumors, such as prostate cancer, breast cancer, small and non-small cell lung cancer and pancreatic cancer. This observation has been used for designing cell markers, but it has not been yet exploited for therapeutical purposes. Despite the enormous biological interest of the peptide, little is known about the stereochemical features that contribute to their activity. On the one hand, mutagenesis studies identified a few receptor residues important for high bombesin affinity and on the other, a few studies focused on the relevance of diverse residues of the peptide for receptor activation. Models of the peptide bound to BB1R and BB2R can be helpful to improve our understanding of the stereochemical features granting bombesin activity. Accordingly, the present study describes the computational process followed to construct such models by means of Steered Molecular Dynamics, using models of the peptide and its receptors. Present results provide new insights into the structure-activity relationships of bombesin and its receptors, as well as render an explanation for the differential binding affinity observed towards BB1R and BB2R. Finally, these models can be further exploited to help for designing novel small molecule peptidomimetics with improved pharmacokinetics profile.
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Affiliation(s)
- Guillem Vila-Julià
- Department of Materials Science and Physical Chemistry, University of Barcelona and the Institut de Recerca en Quimica Teorica i Computacional (IQTCUB), Barcelona, Spain; Department of Chemical Engineering, Universitat Politecnica de Catalunya- Barcelona Tech., Av. Diagonal, 647, 08028 Barcelona, Spain
| | - Jaime Rubio-Martinez
- Department of Materials Science and Physical Chemistry, University of Barcelona and the Institut de Recerca en Quimica Teorica i Computacional (IQTCUB), Barcelona, Spain
| | - Juan J Perez
- Department of Chemical Engineering, Universitat Politecnica de Catalunya- Barcelona Tech., Av. Diagonal, 647, 08028 Barcelona, Spain.
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30
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Pacalon J, Audic G, Magnat J, Philip M, Golebiowski J, Moreau CJ, Topin J. Elucidation of the structural basis for ligand binding and translocation in conserved insect odorant receptor co-receptors. Nat Commun 2023; 14:8182. [PMID: 38081900 PMCID: PMC10713630 DOI: 10.1038/s41467-023-44058-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
In numerous insects, the olfactory receptor family forms a unique class of heteromeric cation channels. Recent progress in resolving the odorant receptor structures offers unprecedented opportunities for deciphering their molecular mechanisms of ligand recognition. Unexpectedly, these structures in apo or ligand-bound states did not reveal the pathway taken by the ligands between the extracellular space and the deep internal cavities. By combining molecular modeling with electrophysiological recordings, we identified amino acids involved in the dynamic entry pathway and the binding of VUAA1 to Drosophila melanogaster's odorant receptor co-receptor (Orco). Our results provide evidence for the exact location of the agonist binding site and a detailed and original mechanism of ligand translocation controlled by a network of conserved residues. These findings would explain the particularly high selectivity of Orcos for their ligands.
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Affiliation(s)
- Jody Pacalon
- Université Côte d'Azur, Institut de Chimie de Nice UMR7272, CNRS, Nice, France
| | | | | | - Manon Philip
- Univ. Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Jérôme Golebiowski
- Department of Brain & Cognitive Sciences, DGIST, 333, Techno JungAng, Daero, HyeongPoong Myeon, Daegu, Republic of Korea
| | | | - Jérémie Topin
- Université Côte d'Azur, Institut de Chimie de Nice UMR7272, CNRS, Nice, France.
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31
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Muratspahić E, Deibler K, Han J, Tomašević N, Jadhav KB, Olivé-Marti AL, Hochrainer N, Hellinger R, Koehbach J, Fay JF, Rahman MH, Hegazy L, Craven TW, Varga BR, Bhardwaj G, Appourchaux K, Majumdar S, Muttenthaler M, Hosseinzadeh P, Craik DJ, Spetea M, Che T, Baker D, Gruber CW. Design and structural validation of peptide-drug conjugate ligands of the kappa-opioid receptor. Nat Commun 2023; 14:8064. [PMID: 38052802 PMCID: PMC10698194 DOI: 10.1038/s41467-023-43718-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 11/17/2023] [Indexed: 12/07/2023] Open
Abstract
Despite the increasing number of GPCR structures and recent advances in peptide design, the development of efficient technologies allowing rational design of high-affinity peptide ligands for single GPCRs remains an unmet challenge. Here, we develop a computational approach for designing conjugates of lariat-shaped macrocyclized peptides and a small molecule opioid ligand. We demonstrate its feasibility by discovering chemical scaffolds for the kappa-opioid receptor (KOR) with desired pharmacological activities. The designed De Novo Cyclic Peptide (DNCP)-β-naloxamine (NalA) exhibit in vitro potent mixed KOR agonism/mu-opioid receptor (MOR) antagonism, nanomolar binding affinity, selectivity, and efficacy bias at KOR. Proof-of-concept in vivo efficacy studies demonstrate that DNCP-β-NalA(1) induces a potent KOR-mediated antinociception in male mice. The high-resolution cryo-EM structure (2.6 Å) of the DNCP-β-NalA-KOR-Gi1 complex and molecular dynamics simulations are harnessed to validate the computational design model. This reveals a network of residues in ECL2/3 and TM6/7 controlling the intrinsic efficacy of KOR. In general, our computational de novo platform overcomes extensive lead optimization encountered in ultra-large library docking and virtual small molecule screening campaigns and offers innovation for GPCR ligand discovery. This may drive the development of next-generation therapeutics for medical applications such as pain conditions.
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Affiliation(s)
- Edin Muratspahić
- Center for Physiology and Pharmacology, Institute of Pharmacology, Medical University of Vienna, 1090, Vienna, Austria
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Kristine Deibler
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
- Novo Nordisk Research Center Seattle, Novo Nordisk A/S, 530 Fairview Ave N #5000, Seattle, WA, 97403, USA
| | - Jianming Han
- Center for Clinical Pharmacology, University of Health Sciences & Pharmacy at St. Louis and Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Nataša Tomašević
- Center for Physiology and Pharmacology, Institute of Pharmacology, Medical University of Vienna, 1090, Vienna, Austria
| | - Kirtikumar B Jadhav
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, 1090, Vienna, Austria
| | - Aina-Leonor Olivé-Marti
- Department of Pharmaceutical Chemistry, Institute of Pharmacy and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
| | - Nadine Hochrainer
- Department of Pharmaceutical Chemistry, Institute of Pharmacy and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
| | - Roland Hellinger
- Center for Physiology and Pharmacology, Institute of Pharmacology, Medical University of Vienna, 1090, Vienna, Austria
| | - Johannes Koehbach
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD, 4072, Australia
- School of Biomedical Sciences, Faculty for Medicine, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Jonathan F Fay
- Department of Biochemistry and Molecular Biology, University of Maryland Baltimore, Baltimore, MD, 21201, USA
| | - Mohammad Homaidur Rahman
- Department of Pharmaceutical and Administrative Sciences, Saint Louis College of Pharmacy, University of Health Sciences & Pharmacy in St. Louis, St. Louis, MO, 63110, USA
| | - Lamees Hegazy
- Department of Pharmaceutical and Administrative Sciences, Saint Louis College of Pharmacy, University of Health Sciences & Pharmacy in St. Louis, St. Louis, MO, 63110, USA
| | - Timothy W Craven
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Balazs R Varga
- Center for Clinical Pharmacology, University of Health Sciences & Pharmacy at St. Louis and Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Gaurav Bhardwaj
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Kevin Appourchaux
- Center for Clinical Pharmacology, University of Health Sciences & Pharmacy at St. Louis and Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Susruta Majumdar
- Center for Clinical Pharmacology, University of Health Sciences & Pharmacy at St. Louis and Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Markus Muttenthaler
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, 1090, Vienna, Austria
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Parisa Hosseinzadeh
- Department of Bioengineering, Knight Campus, University of Oregon, Eugene, OR, 97403, USA
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Mariana Spetea
- Department of Pharmaceutical Chemistry, Institute of Pharmacy and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
| | - Tao Che
- Center for Clinical Pharmacology, University of Health Sciences & Pharmacy at St. Louis and Washington University School of Medicine, St. Louis, MO, 63110, USA.
- Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO, 63110, USA.
| | - David Baker
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA.
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington, WA, 98195, USA.
| | - Christian W Gruber
- Center for Physiology and Pharmacology, Institute of Pharmacology, Medical University of Vienna, 1090, Vienna, Austria.
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32
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Halim SA, Waqas M, Khan A, Ogaly HA, Othman G, Al-Harrasi A. Identification of potential agonist-like molecules for α2-adrenergic receptor by multi-layer virtual screening to combat sinusitis. Comput Biol Med 2023; 167:107693. [PMID: 37976818 DOI: 10.1016/j.compbiomed.2023.107693] [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: 06/13/2023] [Revised: 10/24/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023]
Abstract
Sinusitis is one of the most common respiratory inflammatory conditions and a significant health issue that affects millions of people worldwide with a global prevalence of 10-15%. The side effects of available drug regimens of sinus infection demand the urgent development of new drug candidates to combat sinusitis. With the aim of identifying new drug-like candidates to control sinus, we have conducted multifold comprehensive screening of drug-like molecules targeting α2-adrenergic receptor (α2-AR), which serve as the primary drug target in sinusitis. By structure-based virtual screening of in-house compound's database, ten molecules (CP1-CP10) with agonistic effects for α2-AR were selected, and their binding mechanism with critical residues of α2-AR and their physicochemical properties were studied. Moreover, the process of receptor activation by these compounds and the conformational changes in α2-AR caused by these molecules, were further explored by molecular dynamic simulation. The MM-PBSA estimated free energies of compounds are higher than that of reference agonist (ΔGTOTAL = -39.0 kcal/mol). Among all, CP2-CP3, CP7-CP8 and CP6 have the highest binding free energies of -78.9 kcal/mol, -77.3 kcal/mol, -75.60 kcal/mol, -64.8 kcal/mol, and -61.6 kcal/mol, respectively. While CP4 (-55.0 kcal/mol), CP5 (-49.2 kcal/mol), CP9 (-54.8 ± 0.07 kcal/mol), CP10 (-56.7 ± 0.10 kcal/mol) and CP1 (-46.0 ± 0.08 kcal/mol) also exhibited significant binding free energies. These energetically favorable binding energies indicate strong binding affinity of our compounds for α2-AR as compared to known partial agonist. Therefore, these molecules can serve as excellent drug-like candidates for sinusitis.
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Affiliation(s)
- Sobia Ahsan Halim
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat Al-Mouz, Nizwa, 616, Oman.
| | - Muhammad Waqas
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat Al-Mouz, Nizwa, 616, Oman; Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, Dhodial, 21120, Pakistan
| | - Ajmal Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat Al-Mouz, Nizwa, 616, Oman
| | - Hanan A Ogaly
- Chemistry Department, College of Science, King Khalid University, Abha, 61421, Saudi Arabia
| | - Gehan Othman
- Biology Department, College of Science, King Khalid University, Abha, 61421, Saudi Arabia
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat Al-Mouz, Nizwa, 616, Oman.
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33
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Tyagi C, Marik T, Szekeres A, Vágvölgyi C, Kredics L, Ötvös F. Modeling the Effect on a Novel Fungal Peptaibol Placed in an All-Atom Bacterial Membrane Mimicking System via Accelerated Molecular Dynamics Simulations. Life (Basel) 2023; 13:2288. [PMID: 38137889 PMCID: PMC10744397 DOI: 10.3390/life13122288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/23/2023] [Accepted: 11/27/2023] [Indexed: 12/24/2023] Open
Abstract
We previously reported on a novel peptaibol, named Tripleurin XIIc (TPN), an 18-residue long sequence produced by the fungus Trichoderma pleuroti. We elucidated its 3D structure via classical and accelerated molecular dynamics simulation (aMD) methods and reported the folding dynamics of TPN in water and chloroform solvents. Peptaibols, in general, are insoluble in water, as they are amphipathic and may prefer hydrophobic environments like transmembrane regions. In this study, we attempted to use aMD simulations to model an all-atom bacterial membrane system while placing a TPN molecule in its vicinity. The results highlighted that TPN was able to introduce some disorder into the membrane and caused lipid clustering. It could also enter the transmembrane region from the water-bilayer interface. The structural dynamics of TPN in the transmembrane region revealed a single energetically stable conformation similar to the one obtained from water and chloroform solvent simulations reported by us previously. However, this linear structure was found to be at the local energy minimum (stable) in water but at a metastable intermediate state (higher energy) in chloroform. Therefore, it could be said that the water solvent can be successfully used for folding simulations of peptaibols.
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Affiliation(s)
- Chetna Tyagi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary; (T.M.); (A.S.); (C.V.); (L.K.)
| | - Tamás Marik
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary; (T.M.); (A.S.); (C.V.); (L.K.)
| | - András Szekeres
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary; (T.M.); (A.S.); (C.V.); (L.K.)
| | - Csaba Vágvölgyi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary; (T.M.); (A.S.); (C.V.); (L.K.)
| | - László Kredics
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary; (T.M.); (A.S.); (C.V.); (L.K.)
| | - Ferenc Ötvös
- Institute of Biochemistry, Biological Research Centre, Temesvári krt. 62, H-6726 Szeged, Hungary;
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34
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Twizerimana AP, Becker D, Zhu S, Luedde T, Gohlke H, Münk C. The cyclophilin A-binding loop of the capsid regulates the human TRIM5α sensitivity of nonpandemic HIV-1. Proc Natl Acad Sci U S A 2023; 120:e2306374120. [PMID: 37983491 PMCID: PMC10691330 DOI: 10.1073/pnas.2306374120] [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: 04/19/2023] [Accepted: 09/26/2023] [Indexed: 11/22/2023] Open
Abstract
The rather few cases of humans infected by HIV-1 N, O, or P raise the question of their incomplete adaptation to humans. We hypothesized that early postentry restrictions may be relevant for the impaired spread of these HIVs. One of the best-characterized species-specific restriction factors is TRIM5α. HIV-1 M can escape human (hu) TRIM5α restriction by binding cyclophilin A (CYPA, also known as PPIA, peptidylprolyl isomerase A) to the so-called CYPA-binding loop of its capsid protein. How non-M HIV-1s interact with huTRIM5α is ill-defined. By testing full-length reporter viruses (Δ env) of HIV-1 N, O, P, and SIVgor (simian IV of gorillas), we found that in contrast to HIV-1 M, the nonpandemic HIVs and SIVgor showed restriction by huTRIM5α. Work to identify capsid residues that mediate susceptibility to huTRIM5α revealed that residue 88 in the capsid CYPA-binding loop was important for such differences. There, HIV-1 M uses alanine to resist, while non-M HIV-1s have either valine or methionine, which avail them for huTRIM5α. Capsid residue 88 determines the sensitivity to TRIM5α in an unknown way. Molecular simulations indicated that capsid residue 88 can affect trans-to-cis isomerization patterns on the capsids of the viruses we tested. These differential CYPA usages by pandemic and nonpandemic HIV-1 suggest that the enzymatic activity of CYPA on the viral core might be important for its protective function against huTRIM5α.
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Affiliation(s)
- Augustin P. Twizerimana
- Clinic of Gastroenterology, Hepatology and Infectious Diseases, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf40225, Germany
| | - Daniel Becker
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf40225, Germany
| | - Shenglin Zhu
- Clinic of Gastroenterology, Hepatology and Infectious Diseases, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf40225, Germany
| | - Tom Luedde
- Clinic of Gastroenterology, Hepatology and Infectious Diseases, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf40225, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf40225, Germany
- Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, Jülich52425, Germany
| | - Carsten Münk
- Clinic of Gastroenterology, Hepatology and Infectious Diseases, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf40225, Germany
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35
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Lin C, Kuffour EO, Fuchs NV, Gertzen CGW, Kaiser J, Hirschenberger M, Tang X, Xu HC, Michel O, Tao R, Haase A, Martin U, Kurz T, Drexler I, Görg B, Lang PA, Luedde T, Sparrer KMJ, Gohlke H, König R, Münk C. Regulation of STING activity in DNA sensing by ISG15 modification. Cell Rep 2023; 42:113277. [PMID: 37864791 DOI: 10.1016/j.celrep.2023.113277] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 09/06/2023] [Accepted: 09/28/2023] [Indexed: 10/23/2023] Open
Abstract
Sensing of human immunodeficiency virus type 1 (HIV-1) DNA is mediated by the cyclic GMP-AMP synthase-stimulator of interferon genes (cGAS-STING) signaling axis. Signal transduction and regulation of this cascade is achieved by post-translational modifications. Here we show that cGAS-STING-dependent HIV-1 sensing requires interferon-stimulated gene 15 (ISG15). ISG15 deficiency inhibits STING-dependent sensing of HIV-1 and STING agonist-induced antiviral response. Upon external stimuli, STING undergoes ISGylation at residues K224, K236, K289, K347, K338, and K370. Inhibition of STING ISGylation at K289 suppresses STING-mediated type Ⅰ interferon induction by inhibiting its oligomerization. Of note, removal of STING ISGylation alleviates gain-of-function phenotype in STING-associated vasculopathy with onset in infancy (SAVI). Molecular modeling suggests that ISGylation of K289 is an important regulator of oligomerization. Taken together, our data demonstrate that ISGylation at K289 is crucial for STING activation and represents an important regulatory step in DNA sensing of viruses and autoimmune responses.
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Affiliation(s)
- Chaohui Lin
- Clinic of Gastroenterology, Hepatology and Infectious Diseases, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Edmund Osei Kuffour
- Clinic of Gastroenterology, Hepatology and Infectious Diseases, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Nina V Fuchs
- Host-Pathogen Interactions, Paul-Ehrlich-Institut, Langen, Germany
| | - Christoph G W Gertzen
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany; Center for Structural Studies (CSS), Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Jesko Kaiser
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | | | - Xiao Tang
- Clinic of Gastroenterology, Hepatology and Infectious Diseases, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Haifeng C Xu
- Department of Molecular Medicine II, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Oliver Michel
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Ronny Tao
- Institute for Virology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Alexandra Haase
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery (HTTG), Hannover Medical School, 30625 Hannover, Germany; REBIRTH-Research Center for Translational and Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Ulrich Martin
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery (HTTG), Hannover Medical School, 30625 Hannover, Germany; REBIRTH-Research Center for Translational and Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany; Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Member of the German Center for Lung Research (DZL), Hannover Medical School, 30625 Hannover, Germany
| | - Thomas Kurz
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Ingo Drexler
- Institute for Virology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Boris Görg
- Clinic of Gastroenterology, Hepatology and Infectious Diseases, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Philipp A Lang
- Department of Molecular Medicine II, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Tom Luedde
- Clinic of Gastroenterology, Hepatology and Infectious Diseases, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | | | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany; Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Renate König
- Host-Pathogen Interactions, Paul-Ehrlich-Institut, Langen, Germany
| | - Carsten Münk
- Clinic of Gastroenterology, Hepatology and Infectious Diseases, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
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36
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Xiong Y, Hu X, Ding J, Wang X, Xue Z, Niu Y, Zhang S, Sun C, Xu W. Mechanical Properties of Low-Molecular-Weight Peptide Hydrogels Improved by Thiol-Ene Click Chemistry. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:16750-16759. [PMID: 37963300 DOI: 10.1021/acs.langmuir.3c01906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Low-molecular-weight peptide hydrogels can be formed by self-assembly through weak interactions, but the application of the hydrogel is influenced by its weak mechanical properties. Therefore, it is important to construct low-molecular-weight peptide hydrogels with excellent mechanical properties. In this work, we designed the pentapeptide molecule Fmoc-FFCKK-OH (abbreviated as FFCKK) with a sulfhydryl group, and another low-molecular-weight cross-linker N,N'-methylenebis(acrylamide) (MBA) was introduced to construct a hydrogel with excellent mechanical properties. The secondary structure change process of FFCKK and the assembly mechanism of hydrogel were analyzed using theoretical calculations and experimental characterizations. The occurrence of thiol-ene click chemistry provides covalent interaction in the hydrogel, and the synergistic effect ofcovalent interaction and hydrogen bonding improves the mechanical properties of the hydrogel by nearly 10-fold. The hydrogel was observed to be able to withstand a stress of 368 Pa and to break in a layer-by-layer manner by compression testing. The micromechanics of the hydrogels were characterized, and the excellent mechanical properties of the hydrogels were confirmed. The synergistic approach provides a new idea for the preparation of low-molecular-weight peptide hydrogels and facilitates the expansion of their potential applications in biomedical fields.
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Affiliation(s)
- Yingshuo Xiong
- School of Chemistry and Materials Science, Ludong University, Yantai 264025, China
| | - Xiaohan Hu
- School of Chemistry and Materials Science, Ludong University, Yantai 264025, China
| | - Junjie Ding
- School of Chemistry and Materials Science, Ludong University, Yantai 264025, China
| | - Xinze Wang
- School of Chemistry and Materials Science, Ludong University, Yantai 264025, China
| | - Zhongxin Xue
- School of Chemistry and Materials Science, Ludong University, Yantai 264025, China
| | - Yuzhong Niu
- School of Chemistry and Materials Science, Ludong University, Yantai 264025, China
| | - Shaohua Zhang
- School of Chemistry and Materials Science, Ludong University, Yantai 264025, China
| | - Changmei Sun
- School of Chemistry and Materials Science, Ludong University, Yantai 264025, China
| | - Wenlong Xu
- School of Chemistry and Materials Science, Ludong University, Yantai 264025, China
- Shandong Laboratory of Advanced Materials and Green Manufacturing at Yantai, Yantai 264000, China
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37
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Papadourakis M, Sinenka H, Matricon P, Hénin J, Brannigan G, Pérez-Benito L, Pande V, van Vlijmen H, de Graaf C, Deflorian F, Tresadern G, Cecchini M, Cournia Z. Alchemical Free Energy Calculations on Membrane-Associated Proteins. J Chem Theory Comput 2023; 19:7437-7458. [PMID: 37902715 PMCID: PMC11017255 DOI: 10.1021/acs.jctc.3c00365] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Indexed: 10/31/2023]
Abstract
Membrane proteins have diverse functions within cells and are well-established drug targets. The advances in membrane protein structural biology have revealed drug and lipid binding sites on membrane proteins, while computational methods such as molecular simulations can resolve the thermodynamic basis of these interactions. Particularly, alchemical free energy calculations have shown promise in the calculation of reliable and reproducible binding free energies of protein-ligand and protein-lipid complexes in membrane-associated systems. In this review, we present an overview of representative alchemical free energy studies on G-protein-coupled receptors, ion channels, transporters as well as protein-lipid interactions, with emphasis on best practices and critical aspects of running these simulations. Additionally, we analyze challenges and successes when running alchemical free energy calculations on membrane-associated proteins. Finally, we highlight the value of alchemical free energy calculations calculations in drug discovery and their applicability in the pharmaceutical industry.
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Affiliation(s)
- Michail Papadourakis
- Biomedical
Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527 Athens, Greece
| | - Hryhory Sinenka
- Institut
de Chimie de Strasbourg, UMR7177, CNRS, Université de Strasbourg, F-67083 Strasbourg Cedex, France
| | - Pierre Matricon
- Sosei
Heptares, Steinmetz Building,
Granta Park, Great Abington, Cambridge CB21 6DG, United
Kingdom
| | - Jérôme Hénin
- Laboratoire
de Biochimie Théorique UPR 9080, CNRS and Université Paris Cité, 75005 Paris, France
| | - Grace Brannigan
- Center
for Computational and Integrative Biology, Rutgers University−Camden, Camden, New Jersey 08103, United States of America
- Department
of Physics, Rutgers University−Camden, Camden, New Jersey 08102, United States
of America
| | - Laura Pérez-Benito
- CADD,
In Silico Discovery, Janssen Research &
Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Vineet Pande
- CADD,
In Silico Discovery, Janssen Research &
Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Herman van Vlijmen
- CADD,
In Silico Discovery, Janssen Research &
Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Chris de Graaf
- Sosei
Heptares, Steinmetz Building,
Granta Park, Great Abington, Cambridge CB21 6DG, United
Kingdom
| | - Francesca Deflorian
- Sosei
Heptares, Steinmetz Building,
Granta Park, Great Abington, Cambridge CB21 6DG, United
Kingdom
| | - Gary Tresadern
- CADD,
In Silico Discovery, Janssen Research &
Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Marco Cecchini
- Institut
de Chimie de Strasbourg, UMR7177, CNRS, Université de Strasbourg, F-67083 Strasbourg Cedex, France
| | - Zoe Cournia
- Biomedical
Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527 Athens, Greece
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38
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Case D, Aktulga HM, Belfon K, Cerutti DS, Cisneros GA, Cruzeiro VD, Forouzesh N, Giese TJ, Götz AW, Gohlke H, Izadi S, Kasavajhala K, Kaymak MC, King E, Kurtzman T, Lee TS, Li P, Liu J, Luchko T, Luo R, Manathunga M, Machado MR, Nguyen HM, O’Hearn KA, Onufriev AV, Pan F, Pantano S, Qi R, Rahnamoun A, Risheh A, Schott-Verdugo S, Shajan A, Swails J, Wang J, Wei H, Wu X, Wu Y, Zhang S, Zhao S, Zhu Q, Cheatham TE, Roe DR, Roitberg A, Simmerling C, York DM, Nagan MC, Merz KM. AmberTools. J Chem Inf Model 2023; 63:6183-6191. [PMID: 37805934 PMCID: PMC10598796 DOI: 10.1021/acs.jcim.3c01153] [Citation(s) in RCA: 193] [Impact Index Per Article: 193.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Indexed: 10/10/2023]
Abstract
AmberTools is a free and open-source collection of programs used to set up, run, and analyze molecular simulations. The newer features contained within AmberTools23 are briefly described in this Application note.
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Affiliation(s)
- David
A. Case
- Department
of Chemistry and Chemical Biology, Rutgers
University, Piscataway 08854, New Jersey, United States
| | - Hasan Metin Aktulga
- Department
of Computer Science and Engineering, Michigan
State University, East Lansing 48824-1322, Michigan, United States
| | - Kellon Belfon
- FOG
Pharmaceuticals Inc., Cambridge 02140, Massachusetts, United States
| | - David S. Cerutti
- Psivant, 451 D Street, Suite 205, Boston 02210, Massachusetts, United States
| | - G. Andrés Cisneros
- Department
of Physics, Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson 75801, Texas, United States
| | - Vinícius
Wilian D. Cruzeiro
- Department
of Chemistry and The PULSE Institute, Stanford
University, Stanford 94305, California, United States
| | - Negin Forouzesh
- Department
of Computer Science, California State University, Los Angeles 90032, California, United States
| | - Timothy J. Giese
- Laboratory
for Biomolecular Simulation Research, Institute for Quantitative Biomedicine
and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway 08854, New Jersey, United States
| | - Andreas W. Götz
- San
Diego Supercomputer Center, University of
California San Diego, La Jolla 92093-0505, California, United States
| | - Holger Gohlke
- Institute
for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
- Institute
of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, Jülich 52425, Germany
| | - Saeed Izadi
- Pharmaceutical
Development, Genentech, Inc., South San Francisco 94080, California, United
States
| | - Koushik Kasavajhala
- Laufer
Center for Physical and Quantitative Biology, Department of Chemistry, Stony Brook University, Stony Brook 11794, New York, United States
| | - Mehmet C. Kaymak
- Department
of Computer Science and Engineering, Michigan
State University, East Lansing 48824-1322, Michigan, United States
| | - Edward King
- Departments
of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering,
Materials Science and Engineering, and Biomedical Engineering, Graduate
Program in Chemical and Materials Physics, University of California, Irvine 92697, California, United States
| | - Tom Kurtzman
- Ph.D.
Programs in Chemistry, Biochemistry, and Biology, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York 10016, New York, United States
- Department
of Chemistry, Lehman College, 250 Bedford Park Blvd West, Bronx 10468, New York, United States
| | - Tai-Sung Lee
- Laboratory
for Biomolecular Simulation Research, Institute for Quantitative Biomedicine
and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway 08854, New Jersey, United States
| | - Pengfei Li
- Department
of Chemistry and Biochemistry, Loyola University
Chicago, Chicago 60660, Illinois, United States
| | - Jian Liu
- Beijing
National Laboratory for Molecular Sciences, Institute of Theoretical
and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Tyler Luchko
- Department
of Physics and Astronomy, California State
University, Northridge, Northridge 91330, California, United States
| | - Ray Luo
- Departments
of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering,
Materials Science and Engineering, and Biomedical Engineering, Graduate
Program in Chemical and Materials Physics, University of California, Irvine 92697, California, United States
| | - Madushanka Manathunga
- Department
of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing 48824-1322, Michigan, United States
| | | | - Hai Minh Nguyen
- Department
of Chemistry and Chemical Biology, Rutgers
University, Piscataway 08854, New Jersey, United States
| | - Kurt A. O’Hearn
- Department
of Computer Science and Engineering, Michigan
State University, East Lansing 48824-1322, Michigan, United States
| | - Alexey V. Onufriev
- Departments
of Computer Science and Physics, Virginia
Tech, Blacksburg 24061, Virginia, United
States
| | - Feng Pan
- Department
of Statistics, Florida State University, Tallahassee 32304, Florida, United States
| | - Sergio Pantano
- Institut Pasteur de Montevideo, Montevideo 11400, Uruguay
| | - Ruxi Qi
- Cryo-EM
Center, Southern University of Science and
Technology, Shenzhen 518055, China
| | - Ali Rahnamoun
- Department
of Computer Science and Engineering, Michigan
State University, East Lansing 48824-1322, Michigan, United States
| | - Ali Risheh
- Department
of Computer Science, California State University, Los Angeles 90032, California, United States
| | - Stephan Schott-Verdugo
- Institute
of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, Jülich 52425, Germany
| | - Akhil Shajan
- Department
of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing 48824-1322, Michigan, United States
| | - Jason Swails
- Entos, 4470 W Sunset
Blvd, Suite 107, Los Angeles 90027, California, United States
| | - Junmei Wang
- Department
of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh 15261, Pennsylvania, United States
| | - Haixin Wei
- Departments
of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering,
Materials Science and Engineering, and Biomedical Engineering, Graduate
Program in Chemical and Materials Physics, University of California, Irvine 92697, California, United States
| | - Xiongwu Wu
- Laboratory
of Computational Biology, NHLBI, NIH, Bethesda 20892, Maryland, United States
| | - Yongxian Wu
- Departments
of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering,
Materials Science and Engineering, and Biomedical Engineering, Graduate
Program in Chemical and Materials Physics, University of California, Irvine 92697, California, United States
| | - Shi Zhang
- Laboratory
for Biomolecular Simulation Research, Institute for Quantitative Biomedicine
and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway 08854, New Jersey, United States
| | - Shiji Zhao
- Departments
of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering,
Materials Science and Engineering, and Biomedical Engineering, Graduate
Program in Chemical and Materials Physics, University of California, Irvine 92697, California, United States
- Nurix Therapeutics, Inc., San Francisco 94158, California, United States
| | - Qiang Zhu
- Departments
of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering,
Materials Science and Engineering, and Biomedical Engineering, Graduate
Program in Chemical and Materials Physics, University of California, Irvine 92697, California, United States
| | - Thomas E. Cheatham
- Department
of Medicinal Chemistry, The University of
Utah, 30 South 2000 East, Salt Lake City 84112, Utah, United
States
| | - Daniel R. Roe
- Laboratory
of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda 20892, Maryland, United States
| | - Adrian Roitberg
- Department
of Chemistry, The University of Florida, 440 Leigh Hall, Gainesville 32611-7200, Florida, United States
| | - Carlos Simmerling
- Laufer
Center for Physical and Quantitative Biology, Department of Chemistry, Stony Brook University, Stony Brook 11794, New York, United States
| | - Darrin M. York
- Laboratory
for Biomolecular Simulation Research, Institute for Quantitative Biomedicine
and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway 08854, New Jersey, United States
| | - Maria C. Nagan
- Department
of Chemistry, Stony Brook University, Stony Brook 11794, New York, United States
| | - Kenneth M. Merz
- Department
of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing 48824-1322, Michigan, United States
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39
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Verma P, Kwansa AL, Ho R, Yingling YG, Zimmer J. Insights into substrate coordination and glycosyl transfer of poplar cellulose synthase-8. Structure 2023; 31:1166-1173.e6. [PMID: 37572661 PMCID: PMC10592267 DOI: 10.1016/j.str.2023.07.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 05/19/2023] [Accepted: 07/19/2023] [Indexed: 08/14/2023]
Abstract
Cellulose is an abundant cell wall component of land plants. It is synthesized from UDP-activated glucose molecules by cellulose synthase, a membrane-integrated processive glycosyltransferase. Cellulose synthase couples the elongation of the cellulose polymer with its translocation across the plasma membrane. Here, we present substrate- and product-bound cryogenic electron microscopy structures of the homotrimeric cellulose synthase isoform-8 (CesA8) from hybrid aspen (poplar). UDP-glucose binds to a conserved catalytic pocket adjacent to the entrance to a transmembrane channel. The substrate's glucosyl unit is coordinated by conserved residues of the glycosyltransferase domain and amphipathic interface helices. Site-directed mutagenesis of a conserved gating loop capping the active site reveals its critical function for catalytic activity. Molecular dynamics simulations reveal prolonged interactions of the gating loop with the substrate molecule, particularly across its central conserved region. These transient interactions likely facilitate the proper positioning of the substrate molecule for glycosyl transfer and cellulose translocation.
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Affiliation(s)
- Preeti Verma
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903, USA
| | - Albert L Kwansa
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Ruoya Ho
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903, USA; Howard Hughes Medical Institute, University of Virginia, Charlottesville, VA 22903, USA
| | - Yaroslava G Yingling
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Jochen Zimmer
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903, USA; Howard Hughes Medical Institute, University of Virginia, Charlottesville, VA 22903, USA.
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40
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Yu Z, Ma W, Ji H, Fan Y, Zhao W. Interaction mechanism of egg derived peptides RVPSL and QIGLF with dipalmitoyl phosphatidylcholine membrane: microcalorimetric and molecular dynamics simulation studies. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2023; 103:6383-6393. [PMID: 37205773 DOI: 10.1002/jsfa.12714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 05/03/2023] [Accepted: 05/17/2023] [Indexed: 05/21/2023]
Abstract
BACKGROUND Egg-derived peptides are becoming increasingly popular due to their biological activity and non-toxic effects. The egg-derived peptides Arg-Val-Pro-Ser-Leu (RVPSL) and Gln-Ile-Gly-Leu-Phe (QIGLF) display strong angiotensin-converting enzyme inhibitory activity and they can be taken up by intestinal epithelial cells. The interaction of the egg-derived peptides RVPSL and QIGLF with the membrane remains unclear. RESULTS The position and structure of the peptides in the membrane were calculated. The maximum density values of RVPSL and QIGLF were 2.27 and 1.22 nm from the center of the 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine (DPPC) membrane, respectively, indicating that peptides penetrated the membrane-water interface and were embedded in the membrane. The interaction of RVPSL and QIGLF with the DPPC membrane did not affect the average area per lipid or the lipid sequence parameters. The thermodynamic parameters ΔH, ΔG, and ΔS of the interaction between the peptide RVPSL with the DPPC membrane were 17.91 kJ mol-1 , -17.63 kJ mol-1 , 187.5 J mol-1 ·k-1 , respectively. The thermodynamic parameters ΔH, ΔG, and ΔS of the interaction between peptide QIGLF with DPPC membrane were 17.10 kJ mol-1 , -17.12 kJ mol-1 , 114.8 J mol-1 ·k-1 , respectively. CONCLUSION The results indicated that the binding of peptides RVPSL and QIGLF to DPPC is an endothermic, spontaneous, and entropy-driven reaction. The results of the study are relevant to the problem of the low bioavailability of bioactive peptides (BP). © 2023 Society of Chemical Industry.
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Affiliation(s)
- Zhipeng Yu
- School of Food Science and Engineering, Hainan University, Haikou, P. R. China
| | - Wenhao Ma
- College of Food Science and Engineering, Bohai University, Jinzhou, P. R. China
| | - Huizhuo Ji
- College of Food Science and Engineering, Bohai University, Jinzhou, P. R. China
| | - Yue Fan
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xian, P. R. China
| | - Wenzhu Zhao
- School of Food Science and Engineering, Hainan University, Haikou, P. R. China
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41
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Llinas del Torrent C, Raïch I, Gonzalez A, Casajuana-Martin N, Lillo J, Rebassa JB, Ferreiro-Vera C, Sánchez de Medina V, Franco R, Navarro G, Pardo L. The Leu/Val 6.51 Side Chain of Cannabinoid Receptors Regulates the Binding Mode of the Alkyl Chain of Δ 9-Tetrahydrocannabinol. J Chem Inf Model 2023; 63:5927-5935. [PMID: 37644761 PMCID: PMC10523433 DOI: 10.1021/acs.jcim.3c01054] [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: 07/12/2023] [Indexed: 08/31/2023]
Abstract
(-)-Δ9-trans-tetrahydrocannabinol (THC), which is the principal psychoactive constituent of Cannabis, mediates its action by binding to two members of the G-protein-coupled receptor (GPCR) family: the cannabinoid CB1 (CB1R) and CB2 (CB2R) receptors. Molecular dynamics simulations showed that the pentyl chain of THC could adopts an I-shape conformation, filling an intracellular cavity between Phe3.36 and Trp6.48 for initial agonist-induced receptor activation, in CB1R but not in CB2R. This cavity opens to the five-carbon chain of THC by the conformational change of the γ-branched, flexible, Leu6.51 side chain of CB1R, which is not feasible by the β-branched, mode rigid, Val6.51 side chain of CB2R. In agreement with our computational results, THC could not decrease the forskolin-induced cAMP levels in cells expressing mutant CB1RL6.51V receptor but could activate the mutant CB2RV6.51L receptor as efficiently as wild-type CB1R. Additionally, JWH-133, a full CB2R agonist, contains a branched dimethyl moiety in the ligand chain that bridges Phe3.36 and Val6.51 for receptor activation. In this case, the substitution of Val6.51 to Leu in CB2R makes JWH-133 unable to activate CB2RV6.51L. In conclusion, our combined computational and experimental results have shown that the amino acid at position 6.51 is a key additional player in the initial mechanism of activation of GPCRs that recognize signaling molecules derived from lipid species.
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Affiliation(s)
- Claudia Llinas del Torrent
- Laboratory
of Computational Medicine, Biostatistics Unit, Faculty of Medicine, Universitat Autònoma Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Iu Raïch
- Department
of Biochemistry and Molecular Biomedicine, School of Biology, University of Barcelona, 08028 Barcelona, Spain
- Centro
de Investigación en Red, Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, 28031 Madrid, Spain
| | - Angel Gonzalez
- Laboratory
of Computational Medicine, Biostatistics Unit, Faculty of Medicine, Universitat Autònoma Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Nil Casajuana-Martin
- Laboratory
of Computational Medicine, Biostatistics Unit, Faculty of Medicine, Universitat Autònoma Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Jaume Lillo
- Department
of Biochemistry and Physiology, Faculty of Pharmacy and Food Sciences, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Joan Biel Rebassa
- Department
of Biochemistry and Physiology, Faculty of Pharmacy and Food Sciences, Universitat de Barcelona, 08028 Barcelona, Spain
| | | | | | - Rafael Franco
- Department
of Biochemistry and Molecular Biomedicine, School of Biology, University of Barcelona, 08028 Barcelona, Spain
- Centro
de Investigación en Red, Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, 28031 Madrid, Spain
| | - Gemma Navarro
- Centro
de Investigación en Red, Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, 28031 Madrid, Spain
- Department
of Biochemistry and Physiology, Faculty of Pharmacy and Food Sciences, Universitat de Barcelona, 08028 Barcelona, Spain
- Institute
of Neuroscience, University of Barcelona
(NeuroUB), Av Joan XXIII
27-31, 08028 Barcelona, Spain
| | - Leonardo Pardo
- Laboratory
of Computational Medicine, Biostatistics Unit, Faculty of Medicine, Universitat Autònoma Barcelona, 08193 Bellaterra, Barcelona, Spain
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42
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Kern NR, Lee J, Choi YK, Im W. CHARMM-GUI Multicomponent Assembler for Modeling and Simulation of Complex Multicomponent Systems. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.30.555590. [PMID: 37693396 PMCID: PMC10491218 DOI: 10.1101/2023.08.30.555590] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Atomic-scale molecular modeling and simulation are powerful tools for computational biology. However, constructing models with large, densely packed molecules, non-water solvents, or with combinations of multiple biomembranes, polymers, and nanomaterials remains challenging and requires significant time and expertise. Furthermore, existing tools do not support such assemblies under the periodic boundary conditions (PBC) necessary for molecular simulation. Here, we describe Multicomponent Assembler in CHARMM-GUI that automates complex molecular assembly and simulation input preparation under the PBC. We demonstrate its versatility by preparing 6 challenging systems with varying density of large components: (1) solvated proteins, (2) solvated proteins with a pre-equilibrated membrane, (3) solvated proteins with a sheet-like nanomaterial, (4) solvated proteins with a sheet-like polymer, (5) a mixed membrane-nanomaterial system, and (6) a sheet-like polymer with gaseous solvent. Multicomponent Assembler is expected to be a unique cyberinfrastructure to facilitate innovative studies of complex interactions between small (organic and inorganic) molecules, biomacromolecules, polymers, and nanomaterials.
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Affiliation(s)
- Nathan R. Kern
- Department of Computer Science & Engineering, Lehigh University, Bethlehem, PA, USA
| | - Jumin Lee
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA
| | - Yeol Kyo Choi
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA
| | - Wonpil Im
- Departments of Biological Sciences, Chemistry, Bioengineering, and Computer Science & Engineering, Lehigh University, Bethlehem, PA, USA
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43
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Erlandson SC, Rawson S, Osei-Owusu J, Brock KP, Liu X, Paulo JA, Mintseris J, Gygi SP, Marks DS, Cong X, Kruse AC. The relaxin receptor RXFP1 signals through a mechanism of autoinhibition. Nat Chem Biol 2023; 19:1013-1021. [PMID: 37081311 PMCID: PMC10530065 DOI: 10.1038/s41589-023-01321-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 03/27/2023] [Indexed: 04/22/2023]
Abstract
The relaxin family peptide receptor 1 (RXFP1) is the receptor for relaxin-2, an important regulator of reproductive and cardiovascular physiology. RXFP1 is a multi-domain G protein-coupled receptor (GPCR) with an ectodomain consisting of a low-density lipoprotein receptor class A (LDLa) module and leucine-rich repeats. The mechanism of RXFP1 signal transduction is clearly distinct from that of other GPCRs, but remains very poorly understood. In the present study, we determine the cryo-electron microscopy structure of active-state human RXFP1, bound to a single-chain version of the endogenous agonist relaxin-2 and the heterotrimeric Gs protein. Evolutionary coupling analysis and structure-guided functional experiments reveal that RXFP1 signals through a mechanism of autoinhibition. Our results explain how an unusual GPCR family functions, providing a path to rational drug development targeting the relaxin receptors.
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Affiliation(s)
- Sarah C Erlandson
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Shaun Rawson
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - James Osei-Owusu
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Kelly P Brock
- Department of Systems Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Xinyue Liu
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Joao A Paulo
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Julian Mintseris
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Steven P Gygi
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Debora S Marks
- Department of Systems Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Xiaojing Cong
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Andrew C Kruse
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
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44
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da Justa HC, Hernández González JE, Vuitika L, Mariutti RB, Magnago PAM, de Moraes FR, Senff-Ribeiro A, Gremski LH, Arni RK, Veiga SS. Comparative Biochemical, Structural, and Functional Analysis of Recombinant Phospholipases D from Three Loxosceles Spider Venoms. Int J Mol Sci 2023; 24:12006. [PMID: 37569382 PMCID: PMC10419089 DOI: 10.3390/ijms241512006] [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: 05/08/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/13/2023] Open
Abstract
Spiders of Loxosceles genus are widely distributed and their venoms contain phospholipases D (PLDs), which degrade phospholipids and trigger inflammatory responses, dermonecrosis, hematological changes, and renal injuries. Biochemical, functional, and structural properties of three recombinant PLDs from L. intermedia, L. laeta, and L. gaucho, the principal species clinically relevant in South America, were analyzed. Sera against L. gaucho and L. laeta PLDs strongly cross-reacted with other PLDs, but sera against L. intermedia PLD mostly reacted with homologous molecules, suggesting underlying structural and functional differences. PLDs presented a similar secondary structure profile but distinct melting temperatures. Different methods demonstrated that all PLDs cleave sphingomyelin and lysophosphatidylcholine, but L. gaucho and L. laeta PLDs excelled. L. gaucho PLD showed greater "in vitro" hemolytic activity. L. gaucho and L. laeta PLDs were more lethal in assays with mice and crickets. Molecular dynamics simulations correlated their biochemical activities with differences in sequences and conformations of specific surface loops, which play roles in protein stability and in modulating interactions with the membrane. Despite the high similarity, PLDs from L. gaucho and L. laeta venoms are more active than L. intermedia PLD, requiring special attention from physicians when these two species prevail in endemic regions.
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Affiliation(s)
- Hanna Câmara da Justa
- Department of Cell Biology, Federal University of Paraná (UFPR), Curitiba 81531-980, Brazil; (H.C.d.J.); (L.V.); (P.A.M.M.); (A.S.-R.); (L.H.G.)
| | - Jorge Enrique Hernández González
- Department of Physics, Multi-User Center for Biomolecular Innovation, State University of São Paulo (UNESP), São Paulo 05315-970, Brazil; (J.E.H.G.); (R.B.M.); (F.R.d.M.); (R.K.A.)
| | - Larissa Vuitika
- Department of Cell Biology, Federal University of Paraná (UFPR), Curitiba 81531-980, Brazil; (H.C.d.J.); (L.V.); (P.A.M.M.); (A.S.-R.); (L.H.G.)
- Department of Immunology, Institute of Biomedical Sciences IV, University of São Paulo (ICB-IV/USP), São Paulo 05508-000, Brazil
| | - Ricardo Barros Mariutti
- Department of Physics, Multi-User Center for Biomolecular Innovation, State University of São Paulo (UNESP), São Paulo 05315-970, Brazil; (J.E.H.G.); (R.B.M.); (F.R.d.M.); (R.K.A.)
| | - Pedro Augusto Martinho Magnago
- Department of Cell Biology, Federal University of Paraná (UFPR), Curitiba 81531-980, Brazil; (H.C.d.J.); (L.V.); (P.A.M.M.); (A.S.-R.); (L.H.G.)
| | - Fábio Rogério de Moraes
- Department of Physics, Multi-User Center for Biomolecular Innovation, State University of São Paulo (UNESP), São Paulo 05315-970, Brazil; (J.E.H.G.); (R.B.M.); (F.R.d.M.); (R.K.A.)
| | - Andrea Senff-Ribeiro
- Department of Cell Biology, Federal University of Paraná (UFPR), Curitiba 81531-980, Brazil; (H.C.d.J.); (L.V.); (P.A.M.M.); (A.S.-R.); (L.H.G.)
| | - Luiza Helena Gremski
- Department of Cell Biology, Federal University of Paraná (UFPR), Curitiba 81531-980, Brazil; (H.C.d.J.); (L.V.); (P.A.M.M.); (A.S.-R.); (L.H.G.)
| | - Raghuvir Krishnaswamy Arni
- Department of Physics, Multi-User Center for Biomolecular Innovation, State University of São Paulo (UNESP), São Paulo 05315-970, Brazil; (J.E.H.G.); (R.B.M.); (F.R.d.M.); (R.K.A.)
| | - Silvio Sanches Veiga
- Department of Cell Biology, Federal University of Paraná (UFPR), Curitiba 81531-980, Brazil; (H.C.d.J.); (L.V.); (P.A.M.M.); (A.S.-R.); (L.H.G.)
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45
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Nguyen ATP, Weigle AT, Shukla D. Functional Regulation of Aquaporin Dynamics by Lipid Bilayer Composition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.20.549977. [PMID: 37502896 PMCID: PMC10370204 DOI: 10.1101/2023.07.20.549977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
With the diversity of lipid-protein interactions, any observed membrane protein dynamics or functions directly depend on the lipid bilayer selection. However, the implications of lipid bilayer choice are seldom considered unless characteristic lipid-protein interactions have been previously reported. Using molecular dynamics simulation, we characterize the effects of membrane embedding on plant aquaporin SoPIP2;1, which has no reported high-affinity lipid interactions. The regulatory impacts of a realistic lipid bilayer, and nine different homogeneous bilayers, on varying SoPIP2;1 dynamics were examined. We demonstrate that SoPIP2;1s structure, thermodynamics, kinetics, and water transport are altered as a function of each membrane construct's ensemble properties. Notably, the realistic bilayer provides stabilization of non-functional SoPIP2;1 metastable states. Hydrophobic mismatch and lipid order parameter calculations further explain how lipid ensemble properties manipulate SoPIP2;1 behavior. Our results illustrate the importance of careful bilayer selection when studying membrane proteins. To this end, we advise cautionary measures when performing membrane protein molecular dynamics simulations.
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Affiliation(s)
- Anh T P Nguyen
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, IL 61801
| | - Austin T Weigle
- Department of Chemistry, University of Illinois at Urbana-Champaign, IL 61801
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, IL 61801
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, IL 61801
- Department of Bioengineering, University of Illinois at Urbana-Champaign, IL 61801
- Department of Plant Biology, University of Illinois at Urbana-Champaign, IL 61801
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46
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Mills KR, Torabifard H. Uncovering the Mechanism of the Proton-Coupled Fluoride Transport in the CLC F Antiporter. J Chem Inf Model 2023; 63:2445-2455. [PMID: 37053383 DOI: 10.1021/acs.jcim.2c01228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
Fluoride is a natural antibiotic abundantly present in the environment and, in micromolar concentrations, is able to inhibit enzymes necessary for bacteria to survive. However, as is the case with many antibiotics, bacteria have evolved resistance methods, including through the use of recently discovered membrane proteins. One such protein is the CLCF F-/H+ antiporter protein, a member of the CLC superfamily of anion-transport proteins. Though previous studies have examined this F- transporter, many questions are still left unanswered. To reveal details of the transport mechanism used by CLCF, we have employed molecular dynamics simulations and umbrella sampling calculations. Our results have led to several discoveries, including the mechanism of proton import and how it is able to aid in the fluoride export. Additionally, we have determined the role of the previously identified residues Glu118, Glu318, Met79, and Tyr396. This work is among the first studies of the CLCF F-/H+ antiporter and is the first computational investigation to model the full transport process, proposing a mechanism which couples the F- export with the H+ import.
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Affiliation(s)
- Kira R Mills
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Hedieh Torabifard
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
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47
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Valle-León M, Casajuana-Martin N, Del Torrent CL, Argerich J, Gómez-Acero L, Sahlholm K, Ferré S, Pardo L, Ciruela F. Unique effect of clozapine on adenosine A 2A-dopamine D 2 receptor heteromerization. Biomed Pharmacother 2023; 160:114327. [PMID: 36736280 DOI: 10.1016/j.biopha.2023.114327] [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: 10/25/2022] [Revised: 01/21/2023] [Accepted: 01/26/2023] [Indexed: 02/04/2023] Open
Abstract
The striatal dopamine D2 receptor (D2R) is generally accepted to be involved in positive symptoms of schizophrenia and is a main target for clinically used antipsychotics. D2R are highly expressed in the striatum, where they form heteromers with the adenosine A2A receptor (A2AR). Changes in the density of A2AR-D2R heteromers have been reported in postmortem tissue from patients with schizophrenia, but the degree to which A2R are involved in schizophrenia and the effect of antipsychotic drugs is unknown. Here, we examine the effect of exposure to three prototypical antipsychotic drugs on A2AR-D2R heteromerization in mammalian cells using a NanoBiT assay. After 16 h of exposure, a significant increase in the density of A2AR-D2R heteromers was found with haloperidol and aripiprazole, but not with clozapine. On the other hand, clozapine, but not haloperidol or aripiprazole, was associated with a significant decrease in A2AR-D2R heteromerization after 2 h of treatment. Computational binding models of these compounds revealed distinctive molecular signatures that explain their different influence on heteromerization. The bulky tricyclic moiety of clozapine displaces TM 5 of D2R, inducing a clash with A2AR, while the extended binding mode of haloperidol and aripiprazole stabilizes a specific conformation of the second extracellular loop of D2R that enhances the interaction with A2AR. It is proposed that an increase in A2AR-D2R heteromerization is involved in the extrapyramidal side effects (EPS) of antipsychotics and that the specific clozapine-mediated destabilization of A2AR-D2R heteromerization can explain its low EPS liability.
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Affiliation(s)
- Marta Valle-León
- Pharmacology Unit, Department of Pathology and Experimental Therapeutics, School of Medicine and Health Sciences, Institute of Neurosciences, University of Barcelona, 08907 L'Hospitalet de Llobregat, Spain; Neuropharmacology and Pain Group, Neuroscience Program, Institut d'Investigació Biomèdica de Bellvitge, IDIBELL, 08907 L'Hospitalet de Llobregat, Spain
| | - Nil Casajuana-Martin
- Laboratory of Computational Medicine, Biostatistics Unit, Faculty of Medicine, Universitat Autònoma Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Claudia Llinas Del Torrent
- Laboratory of Computational Medicine, Biostatistics Unit, Faculty of Medicine, Universitat Autònoma Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Josep Argerich
- Pharmacology Unit, Department of Pathology and Experimental Therapeutics, School of Medicine and Health Sciences, Institute of Neurosciences, University of Barcelona, 08907 L'Hospitalet de Llobregat, Spain; Neuropharmacology and Pain Group, Neuroscience Program, Institut d'Investigació Biomèdica de Bellvitge, IDIBELL, 08907 L'Hospitalet de Llobregat, Spain
| | - Laura Gómez-Acero
- Pharmacology Unit, Department of Pathology and Experimental Therapeutics, School of Medicine and Health Sciences, Institute of Neurosciences, University of Barcelona, 08907 L'Hospitalet de Llobregat, Spain; Neuropharmacology and Pain Group, Neuroscience Program, Institut d'Investigació Biomèdica de Bellvitge, IDIBELL, 08907 L'Hospitalet de Llobregat, Spain
| | - Kristoffer Sahlholm
- Pharmacology Unit, Department of Pathology and Experimental Therapeutics, School of Medicine and Health Sciences, Institute of Neurosciences, University of Barcelona, 08907 L'Hospitalet de Llobregat, Spain; Neuropharmacology and Pain Group, Neuroscience Program, Institut d'Investigació Biomèdica de Bellvitge, IDIBELL, 08907 L'Hospitalet de Llobregat, Spain; Department of Integrative Medical Biology, Wallenberg Centre for Molecular Medicine, Umeå University, 907 87 Umeå, Sweden; Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Sergi Ferré
- Integrative Neurobiology Section, National Institute on Drug Abuse, Intramural Research Program, National Institutes of Health, Baltimore, MD, USA.
| | - Leonardo Pardo
- Laboratory of Computational Medicine, Biostatistics Unit, Faculty of Medicine, Universitat Autònoma Barcelona, Bellaterra, 08193 Barcelona, Spain.
| | - Francisco Ciruela
- Pharmacology Unit, Department of Pathology and Experimental Therapeutics, School of Medicine and Health Sciences, Institute of Neurosciences, University of Barcelona, 08907 L'Hospitalet de Llobregat, Spain; Neuropharmacology and Pain Group, Neuroscience Program, Institut d'Investigació Biomèdica de Bellvitge, IDIBELL, 08907 L'Hospitalet de Llobregat, Spain.
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48
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Reiter S, Kiss FL, Hauer J, de Vivie-Riedle R. Thermal site energy fluctuations in photosystem I: new insights from MD/QM/MM calculations. Chem Sci 2023; 14:3117-3131. [PMID: 36970098 PMCID: PMC10034153 DOI: 10.1039/d2sc06160k] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 02/03/2023] [Indexed: 02/09/2023] Open
Abstract
Cyanobacterial photosystem I (PSI) is one of the most efficient photosynthetic machineries found in nature. Due to the large scale and complexity of the system, the energy transfer mechanism from the antenna complex to the reaction center is still not fully understood. A central element is the accurate evaluation of the individual chlorophyll excitation energies (site energies). Such an evaluation must include a detailed treatment of site specific environmental influences on structural and electrostatic properties, but also their evolution in the temporal domain, because of the dynamic nature of the energy transfer process. In this work, we calculate the site energies of all 96 chlorophylls in a membrane-embedded model of PSI. The employed hybrid QM/MM approach using the multireference DFT/MRCI method in the QM region allows to obtain accurate site energies under explicit consideration of the natural environment. We identify energy traps and barriers in the antenna complex and discuss their implications for energy transfer to the reaction center. Going beyond previous studies, our model also accounts for the molecular dynamics of the full trimeric PSI complex. Via statistical analysis we show that the thermal fluctuations of single chlorophylls prevent the formation of a single prominent energy funnel within the antenna complex. These findings are also supported by a dipole exciton model. We conclude that energy transfer pathways may form only transiently at physiological temperatures, as thermal fluctuations overcome energy barriers. The set of site energies provided in this work sets the stage for theoretical and experimental studies on the highly efficient energy transfer mechanisms in PSI.
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Affiliation(s)
- Sebastian Reiter
- Department of Chemistry, Ludwig-Maximilians-Universität München Butenandtstr. 11 81377 Munich Germany
| | - Ferdinand L Kiss
- Department of Chemistry, Ludwig-Maximilians-Universität München Butenandtstr. 11 81377 Munich Germany
| | - Jürgen Hauer
- Department of Chemistry, Technical University of Munich Lichtenbergstr. 4, Garching 85747 Germany
| | - Regina de Vivie-Riedle
- Department of Chemistry, Ludwig-Maximilians-Universität München Butenandtstr. 11 81377 Munich Germany
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49
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Verma P, Kwansa AL, Ho R, Yingling YG, Zimmer J. Insights into substrate coordination and glycosyl transfer of poplar cellulose synthase-8. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.07.527505. [PMID: 36798277 PMCID: PMC9934533 DOI: 10.1101/2023.02.07.527505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Cellulose is an abundant cell wall component of land plants. It is synthesized from UDP-activated glucose molecules by cellulose synthase, a membrane-integrated processive glycosyltransferase. Cellulose synthase couples the elongation of the cellulose polymer with its translocation across the plasma membrane. Here, we present substrate and product-bound cryogenic electron microscopy structures of the homotrimeric cellulose synthase isoform-8 (CesA8) from hybrid aspen (poplar). UDP-glucose binds to a conserved catalytic pocket adjacent to the entrance to a transmembrane channel. The substrate's glucosyl unit is coordinated by conserved residues of the glycosyltransferase domain and amphipathic interface helices. Site-directed mutagenesis of a conserved gating loop capping the active site reveals its critical function for catalytic activity. Molecular dynamics simulations reveal prolonged interactions of the gating loop with the substrate molecule, particularly across its central conserved region. These transient interactions likely facilitate the proper positioning of the substrate molecule for glycosyl transfer and cellulose translocation. Highlights Cryo-EM structures of substrate and product bound poplar cellulose synthase provide insights into substrate selectivitySite directed mutagenesis signifies a critical function of the gating loop for catalysisMolecular dynamics simulations support persistent gating loop - substrate interactionsGating loop helps in positioning the substrate molecule to facilitate cellulose elongationConserved cellulose synthesis substrate binding mechanism across the kingdoms.
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Affiliation(s)
- Preeti Verma
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, 22903, USA
| | - Albert L. Kwansa
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Ruoya Ho
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, 22903, USA
- Howard Hughes Medical Institute, University of Virginia, Charlottesville, VA 22903
| | - Yaroslava G. Yingling
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Jochen Zimmer
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, 22903, USA
- Howard Hughes Medical Institute, University of Virginia, Charlottesville, VA 22903
- Lead contact
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50
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Meng Y, Liu R, Wang L, Li F, Tian Y, Lu H. Binding affinity and conformational change predictions for a series of inhibitors with RuBisCO in a carbon dioxide gas and water environment by multiple computational methods. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2023.121478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
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