1
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Stein C. Effects of pH on opioid receptor activation and implications for drug design. Biophys J 2024:S0006-3495(24)00446-6. [PMID: 38970252 DOI: 10.1016/j.bpj.2024.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/29/2024] [Accepted: 07/02/2024] [Indexed: 07/08/2024] Open
Abstract
G-protein-coupled receptors are integral membrane proteins that transduce chemical signals from the extracellular matrix into the cell. Traditional drug design has considered ligand-receptor interactions only under normal conditions. However, studies on opioids indicate that such interactions are very different in diseased tissues. In such microenvironments, protons play an important role in structural and functional alterations of both ligands and receptors. The pertinent literature strongly suggests that future drug design should take these aspects into account in order to reduce adverse side effects while preserving desired effects of novel compounds.
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Affiliation(s)
- Christoph Stein
- Charité Universitätsmedizin Berlin, Campus Benjamin Franklin, Experimental Anaesthesiology, Berlin, Germany.
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2
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Kapur B, Baldessari F, Lazaratos M, Nar H, Schnapp G, Giorgetti A, Bondar AN. Protons taken hostage: Dynamic H-bond networks of the pH-sensing GPR68. Comput Struct Biotechnol J 2023; 21:4370-4384. [PMID: 37711190 PMCID: PMC10498176 DOI: 10.1016/j.csbj.2023.08.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 08/30/2023] [Accepted: 08/30/2023] [Indexed: 09/16/2023] Open
Abstract
Proton-sensing G Protein Coupled Receptors (GPCRs) sense changes in the extracellular pH to effect cell signaling for cellular homeostasis. They tend to be overexpressed in solid tumors associated with acidic extracellular pH, and are of direct interest as drug targets. How proton-sensing GPCRs sense extracellular acidification and activate upon protonation change is important to understand, because it may guide the design of therapeutics. Lack of publicly available experimental structures make it challenging to discriminate between conflicting mechanisms proposed for proton-binding, as main roles have been assigned to either an extracellular histidine cluster or to an internal carboxylic triad. Here we present a protocol to derive and evaluate structural models of the proton-sensing GPR68. This approach integrates state-of-the-art homology modeling with microsecond-timescale atomistic simulations, and with a detailed assessment of the compatibility of the structural models with known structural features of class A GPCRs. To decipher structural elements of potential interest for protonation-coupled conformational changes of GPR68, we used the best-compatible model as a starting point for independent atomistic simulations of GPR68 with different protonation states, and graph computations to characterize the response of GPR68 to changes in protonation. We found that GPR68 hosts an extended hydrogen-bond network that inter-connects the extracellular histidine cluster to the internal carboxylic triad, and which can even reach groups at the cytoplasmic G-protein binding site. Taken together, results suggest that GPR68 relies on dynamic, hydrogen-bond networks to inter-connect extracellular and internal proton-binding sites, and to elicit conformational changes at the cytoplasmic G-protein binding site.
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Affiliation(s)
- Bhav Kapur
- Boehringer-Ingelheim Pharma GmbH & Co. KG, Birkendorfer Straße 65, 88397 Biberach an der Riß, Germany
- Christian-Albrechts-University of Kiel, 24118 Kiel, Germany
| | | | - Michalis Lazaratos
- Department of Physics, Theoretical Molecular Biophysics Group, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
| | - Herbert Nar
- Boehringer-Ingelheim Pharma GmbH & Co. KG, Birkendorfer Straße 65, 88397 Biberach an der Riß, Germany
| | - Gisela Schnapp
- Boehringer-Ingelheim Pharma GmbH & Co. KG, Birkendorfer Straße 65, 88397 Biberach an der Riß, Germany
| | - Alejandro Giorgetti
- University of Verona, Department of Biotechnology, 37134 Verona, Italy
- Forschungszentrum Jülich, Institute for Neuroscience and Medicine and Institute for Advanced Simulations (IAS-5/INM-9), Computational Biomedicine, Wilhelm-Johnen Straße, 52525 Jülich, Germany
| | - Ana-Nicoleta Bondar
- Forschungszentrum Jülich, Institute for Neuroscience and Medicine and Institute for Advanced Simulations (IAS-5/INM-9), Computational Biomedicine, Wilhelm-Johnen Straße, 52525 Jülich, Germany
- University of Bucharest, Faculty of Physics, Str. Atomiştilor 405, 077125 Bucharest-Măgurele, Romania
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3
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Lešnik S, Bren U, Domratcheva T, Bondar AN. Fentanyl and the Fluorinated Fentanyl Derivative NFEPP Elicit Distinct Hydrogen-Bond Dynamics of the Opioid Receptor. J Chem Inf Model 2023; 63:4732-4748. [PMID: 37498626 DOI: 10.1021/acs.jcim.3c00197] [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: 07/28/2023]
Abstract
The development of safe therapeutics to manage pain is of central interest for biomedical applications. The fluorinated fentanyl derivative N-(3-fluoro-1-phenethylpiperidin-4-yl)-N-phenylpropionamide (NFEPP) is potentially a safer alternative to fentanyl because unlike fentanyl─which binds to the μ-opioid receptor (MOR) at both physiological and acidic pH─NFEPP might bind to the MOR only at acidic pH typical of inflamed tissue. Knowledge of the protonation-coupled dynamics of the receptor-drug interactions is thus required to understand the molecular mechanism by which receptor activation initiates cell signaling to silence pain. To this end, here we have carried out extensive atomistic simulations of the MOR in different protonation states, in the absence of opioid drugs, and in the presence of fentanyl vs NFEPP. We used graph-based analyses to characterize internal hydrogen-bond networks that could contribute to the activation of the MOR. We find that fentanyl and NFEPP prefer distinct binding poses and that, in their binding poses, fentanyl and NFEPP partake in distinct internal hydrogen-bond networks, leading to the cytoplasmic G-protein-binding region. Moreover, the protonation state of functionally important aspartic and histidine side chains impacts hydrogen-bond networks that extend throughout the receptor, such that the ligand-bound MOR presents at its cytoplasmic G-protein-binding side, a hydrogen-bonding environment where dynamics depend on whether fentanyl or NFEPP is bound, and on the protonation state of specific MOR groups. The exquisite sensitivity of the internal protein-water hydrogen-bond network to the protonation state and to details of the drug binding could enable the MOR to elicit distinct pH- and opioid-dependent responses at its cytoplasmic G-protein-binding site.
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Affiliation(s)
- Samo Lešnik
- Faculty of Chemistry and Chemical Engineering, Laboratory of Physical Chemistry and Chemical Thermodynamics, University of Maribor, Smetanova ulica 17, SI-2000 Maribor, Slovenia
- Institute for Environmental Protection and Sensors, Beloruska ulica 7, 2000 Maribor, Slovenia
| | - Urban Bren
- Faculty of Chemistry and Chemical Engineering, Laboratory of Physical Chemistry and Chemical Thermodynamics, University of Maribor, Smetanova ulica 17, SI-2000 Maribor, Slovenia
- Institute for Environmental Protection and Sensors, Beloruska ulica 7, 2000 Maribor, Slovenia
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, SI-6000 Koper, Slovenia
| | - Tatiana Domratcheva
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
- Department of Biomolecular Mechanisms, Max-Plank-Institute fur Medizinische Forschung, D-69120 Heidelberg, Germany
| | - Ana-Nicoleta Bondar
- Faculty of Physics, University of Bucharest, Atomiştilor 405, 077125 Măgurele, Romania
- Institute of Computational Biomedicine, IAS-5/INM-9, Forschungszentrum Jülich, Wilhelm-Johnen Straße, 5428 Jülich, Germany
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4
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Papageorgiou L, Christou E, Louka E, Papakonstantinou E, Diakou I, Pierouli K, Dragoumani K, Bacopoulou F, Chrousos GP, Eliopoulos E, Vlachakis D. ADRA2B and HTR1A: An Updated Study of the Biogenic Amine Receptors Reveals Novel Conserved Motifs Which Play Key Role in Mental Disorders. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1423:79-99. [PMID: 37525034 DOI: 10.1007/978-3-031-31978-5_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Mental disorders are strongly connected with several psychiatric conditions including depression, bipolar disorder, schizophrenia, eating disorder, and suicides. There are many biological conditions and pathways that define these complicated illnesses. For example, eating disorders are complex mental health conditions that require the intervention of geneticists, psychiatrists, and medical experts in order to alleviate their symptoms. A patient with suicidal ideation should first be identified and consequently monitored by a similar team of specialists. Both genetics and epigenetics can shed light on eating disorders and suicides as they are found in the main core of such investigations. In the present study, an analysis has been performed on two specific members of the GPCR family toward drawing conclusions regarding their functionality and implementation in mental disorders. Specifically, evolutionary and structural studies on the adrenoceptor alpha 2b (ADRA2B) and the 5-hydroxytryptamine receptor 1A (HTR1A) have been carried out. Both receptors are classified in the biogenic amine receptors sub-cluster of the GPCRs and have been connected in many studies with mental diseases and malnutrition conditions. The major goal of this study is the investigation of conserved motifs among biogenic amine receptors that play an important role in this family signaling pathway, through an updated evolutionary analysis and the correlation of this information with the structural features of the HTR1A and ADRA2B. Furthermore, the structural comparison of ADRA2B, HTR1A, and other members of GPCRs related to mental disorders is performed.
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Affiliation(s)
- Louis Papageorgiou
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Evangelia Christou
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Effrosyni Louka
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Eleni Papakonstantinou
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Io Diakou
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Katerina Pierouli
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Konstantina Dragoumani
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Flora Bacopoulou
- University Research Institute of Maternal and Child Health & Precision Medicine, National and Kapodistrian University of Athens, "Aghia Sophia" Children's Hospital, Athens, Greece
| | - George P Chrousos
- University Research Institute of Maternal and Child Health & Precision Medicine, National and Kapodistrian University of Athens, "Aghia Sophia" Children's Hospital, Athens, Greece
| | - Elias Eliopoulos
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Dimitrios Vlachakis
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece.
- University Research Institute of Maternal and Child Health & Precision Medicine, National and Kapodistrian University of Athens, "Aghia Sophia" Children's Hospital, Athens, Greece.
- Division of Endocrinology and Metabolism, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece.
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5
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Bueschbell B, Manga P, Schiedel AC. The Many Faces of G Protein-Coupled Receptor 143, an Atypical Intracellular Receptor. Front Mol Biosci 2022; 9:873777. [PMID: 35495622 PMCID: PMC9039016 DOI: 10.3389/fmolb.2022.873777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 03/10/2022] [Indexed: 12/24/2022] Open
Abstract
GPCRs transform extracellular stimuli into a physiological response by activating an intracellular signaling cascade initiated via binding to G proteins. Orphan G protein-coupled receptors (GPCRs) hold the potential to pave the way for development of new, innovative therapeutic strategies. In this review we will introduce G protein-coupled receptor 143 (GPR143), an enigmatic receptor in terms of classification within the GPCR superfamily and localization. GPR143 has not been assigned to any of the GPCR families due to the lack of common structural motifs. Hence we will describe the most important motifs of classes A and B and compare them to the protein sequence of GPR143. While a precise function for the receptor has yet to be determined, the protein is expressed abundantly in pigment producing cells. Many GPR143 mutations cause X-linked Ocular Albinism Type 1 (OA1, Nettleship-Falls OA), which results in hypopigmentation of the eyes and loss of visual acuity due to disrupted visual system development and function. In pigment cells of the skin, loss of functional GPR143 results in abnormally large melanosomes (organelles in which pigment is produced). Studies have shown that the receptor is localized internally, including at the melanosomal membrane, where it may function to regulate melanosome size and/or facilitate protein trafficking to the melanosome through the endolysosomal system. Numerous additional roles have been proposed for GPR143 in determining cancer predisposition, regulation of blood pressure, development of macular degeneration and signaling in the brain, which we will briefly describe as well as potential ligands that have been identified. Furthermore, GPR143 is a promiscuous receptor that has been shown to interact with multiple other melanosomal proteins and GPCRs, which strongly suggests that this orphan receptor is likely involved in many different physiological actions.
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Affiliation(s)
- Beatriz Bueschbell
- Department of Pharmaceutical and Medicinal Chemistry, Pharmaceutical Institute, University of Bonn, Bonn, Germany
| | - Prashiela Manga
- Ronald O. Perelman Department of Dermatology, Grossman School of Medicine, New York University, New York City, NY, United States
| | - Anke C. Schiedel
- Department of Pharmaceutical and Medicinal Chemistry, Pharmaceutical Institute, University of Bonn, Bonn, Germany
- *Correspondence: Anke C. Schiedel,
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6
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Bedart C, Renault N, Chavatte P, Porcherie A, Lachgar A, Capron M, Farce A. SINAPs: A Software Tool for Analysis and Visualization of Interaction Networks of Molecular Dynamics Simulations. J Chem Inf Model 2022; 62:1425-1436. [PMID: 35239339 PMCID: PMC8966674 DOI: 10.1021/acs.jcim.1c00854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
As long as the structural study of molecular mechanisms requires multiple molecular dynamics reflecting contrasted bioactive states, the subsequent analysis of molecular interaction networks remains a bottleneck to be fairly treated and requires a user-friendly 3D view of key interactions. Structural Interaction Network Analysis Protocols (SINAPs) is a proprietary python tool developed to (i) quickly solve key interactions able to distinguish two protein states, either from two sets of molecular dynamics simulations or from two crystallographic structures, and (ii) render a user-friendly 3D view of these key interactions through a plugin of UCSF Chimera, one of the most popular open-source viewing software for biomolecular systems. Through two case studies, glucose transporter-1 (GLUT-1) and A2A adenosine receptor (A2AR), SINAPs easily pinpointed key interactions observed experimentally and relevant for their bioactivities. This very effective tool was thus applied to identify the amino acids involved in the molecular enzymatic mechanisms ruling the activation of an immunomodulator drug candidate, P28 glutathione-S-transferase (P28GST). SINAPs is freely available at https://github.com/ParImmune/SINAPs.
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Affiliation(s)
- Corentin Bedart
- Univ.
Lille, Inserm, CHU Lille, U1286 - Infinite - Institute for Translational
Research in Inflammation, F-59000 Lille, France,Par’Immune,
Bio-incubateur Eurasanté, 70 rue du Dr. Yersin, 59120 Loos-Lez-Lille, France,
| | - Nicolas Renault
- Univ.
Lille, Inserm, CHU Lille, U1286 - Infinite - Institute for Translational
Research in Inflammation, F-59000 Lille, France
| | - Philippe Chavatte
- Univ.
Lille, Inserm, CHU Lille, U1286 - Infinite - Institute for Translational
Research in Inflammation, F-59000 Lille, France
| | - Adeline Porcherie
- Par’Immune,
Bio-incubateur Eurasanté, 70 rue du Dr. Yersin, 59120 Loos-Lez-Lille, France
| | - Abderrahim Lachgar
- Par’Immune,
Bio-incubateur Eurasanté, 70 rue du Dr. Yersin, 59120 Loos-Lez-Lille, France
| | - Monique Capron
- Univ.
Lille, Inserm, CHU Lille, U1286 - Infinite - Institute for Translational
Research in Inflammation, F-59000 Lille, France,Par’Immune,
Bio-incubateur Eurasanté, 70 rue du Dr. Yersin, 59120 Loos-Lez-Lille, France
| | - Amaury Farce
- Univ.
Lille, Inserm, CHU Lille, U1286 - Infinite - Institute for Translational
Research in Inflammation, F-59000 Lille, France,
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7
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Bondar AN. Proton-Binding Motifs of Membrane-Bound Proteins: From Bacteriorhodopsin to Spike Protein S. Front Chem 2021; 9:685761. [PMID: 34136464 PMCID: PMC8203321 DOI: 10.3389/fchem.2021.685761] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/18/2021] [Indexed: 11/13/2022] Open
Abstract
Membrane-bound proteins that change protonation during function use specific protein groups to bind and transfer protons. Knowledge of the identity of the proton-binding groups is of paramount importance to decipher the reaction mechanism of the protein, and protonation states of prominent are studied extensively using experimental and computational approaches. Analyses of model transporters and receptors from different organisms, and with widely different biological functions, indicate common structure-sequence motifs at internal proton-binding sites. Proton-binding dynamic hydrogen-bond networks that are exposed to the bulk might provide alternative proton-binding sites and proton-binding pathways. In this perspective article I discuss protonation coupling and proton binding at internal and external carboxylate sites of proteins that use proton transfer for function. An inter-helical carboxylate-hydroxyl hydrogen-bond motif is present at functionally important sites of membrane proteins from archaea to the brain. External carboxylate-containing H-bond clusters are observed at putative proton-binding sites of protonation-coupled model proteins, raising the question of similar functionality in spike protein S.
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Affiliation(s)
- Ana-Nicoleta Bondar
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics Group, Berlin, Germany
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8
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Zhang XC, Zhang H. P-type ATPases use a domain-association mechanism to couple ATP hydrolysis to conformational change. BIOPHYSICS REPORTS 2019. [DOI: 10.1007/s41048-019-0087-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
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9
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Zhang XC, Li H. Interplay between the electrostatic membrane potential and conformational changes in membrane proteins. Protein Sci 2019; 28:502-512. [PMID: 30549351 DOI: 10.1002/pro.3563] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 12/12/2018] [Accepted: 12/13/2018] [Indexed: 12/16/2022]
Abstract
Transmembrane electrostatic membrane potential is a major energy source of the cell. Importantly, it determines the structure as well as function of charge-carrying membrane proteins. Here, we discuss the relationship between membrane potential and membrane proteins, in particular whether the conformation of these proteins is integrally connected to the membrane potential. Together, these concepts provide a framework for rationalizing the types of conformational changes that have been observed in membrane proteins and for better understanding the electrostatic effects of the membrane potential on both reversible as well as unidirectional dynamic processes of membrane proteins.
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Affiliation(s)
- Xuejun C Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hang Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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10
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Zhang XC, Zhou Y, Cao C. Proton transfer during class-A GPCR activation: do the CWxP motif and the membrane potential act in concert? BIOPHYSICS REPORTS 2018. [DOI: 10.1007/s41048-018-0056-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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11
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Liu M, Zhang XC. Energy-coupling mechanism of the multidrug resistance transporter AcrB: Evidence for membrane potential-driving hypothesis through mutagenic analysis. Protein Cell 2018; 8:623-627. [PMID: 28497315 PMCID: PMC5546932 DOI: 10.1007/s13238-017-0417-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- Min Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuejun C Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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12
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Selvam B, Shamsi Z, Shukla D. Universality of the Sodium Ion Binding Mechanism in Class A G-Protein-Coupled Receptors. Angew Chem Int Ed Engl 2018; 57:3048-3053. [DOI: 10.1002/anie.201708889] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 12/20/2017] [Indexed: 11/07/2022]
Affiliation(s)
- Balaji Selvam
- Department of Chemical and Biomolecular Engineering; University of Illinois at Urbana-Champaign; Urbana IL 61801 USA
| | - Zahra Shamsi
- Department of Chemical and Biomolecular Engineering; University of Illinois at Urbana-Champaign; Urbana IL 61801 USA
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering; University of Illinois at Urbana-Champaign; Urbana IL 61801 USA
- Department of Plant Biology, Center for Biophysics & Quantitative Biology, National Center for Supercomputing Applications; University of Illinois at Urbana-Champaign; Urbana IL 61801 USA
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13
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Selvam B, Shamsi Z, Shukla D. Universality of the Sodium Ion Binding Mechanism in Class A G-Protein-Coupled Receptors. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201708889] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Balaji Selvam
- Department of Chemical and Biomolecular Engineering; University of Illinois at Urbana-Champaign; Urbana IL 61801 USA
| | - Zahra Shamsi
- Department of Chemical and Biomolecular Engineering; University of Illinois at Urbana-Champaign; Urbana IL 61801 USA
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering; University of Illinois at Urbana-Champaign; Urbana IL 61801 USA
- Department of Plant Biology, Center for Biophysics & Quantitative Biology, National Center for Supercomputing Applications; University of Illinois at Urbana-Champaign; Urbana IL 61801 USA
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14
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Zhang XC, Liu M, Lu G, Heng J. Thermodynamic secrets of multidrug resistance: A new take on transport mechanisms of secondary active antiporters. Protein Sci 2017; 27:595-613. [PMID: 29193407 DOI: 10.1002/pro.3355] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 11/20/2017] [Accepted: 11/21/2017] [Indexed: 12/17/2022]
Abstract
Multidrug resistance (MDR) presents a growing challenge to global public health. Drug extrusion transporters play a critical part in MDR; thus, their mechanisms of substrate recognition are being studied in great detail. In this work, we review common structural features of key transporters involved in MDR. Based on our membrane potential-driving hypothesis, we propose a general energy-coupling mechanism for secondary-active antiporters. This putative mechanism provides a common framework for understanding poly-specificity of most-if not all-MDR transporters.
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Affiliation(s)
- Xuejun C Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing, 100101, China.,College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Min Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing, 100101, China.,College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guangyuan Lu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing, 100101, China.,College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jie Heng
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing, 100101, China
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15
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Zhang XC, Liu M, Han L. Energy coupling mechanisms of AcrB-like RND transporters. BIOPHYSICS REPORTS 2017; 3:73-84. [PMID: 29238744 PMCID: PMC5719797 DOI: 10.1007/s41048-017-0042-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 07/27/2017] [Indexed: 01/09/2023] Open
Abstract
Prokaryotic AcrB-like proteins belong to a family of transporters of the RND superfamily, and as main contributing factor to multidrug resistance pose a tremendous threat to future human health. A unique feature of AcrB transporters is the presence of two separate domains responsible for carrying substrate and generating energy. Significant progress has been made in elucidating the three-dimensional structures of the homo-trimer complexes of AcrB-like transporters, and a three-step functional rotation was identified for this class of transporters. However, the detailed mechanisms for the transduction of the substrate binding signal, as well as the energy coupling processes between the functionally distinct domains remain to be established. Here, we propose a model for the interdomain communication in AcrB that explains how the substrate binding signal from the substrate-carrier domain triggers protonation in the transmembrane domain. Our model further provides a plausible mechanism that explains how protonation induces conformational changes in the substrate-carrier domain. We summarize the thermodynamic principles that govern the functional cycle of the AcrB trimer complex.
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Affiliation(s)
- Xuejun C Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China.,College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Min Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China.,College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Lei Han
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China.,College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049 China
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16
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Zhang XC, Liu Z, Li J. From membrane tension to channel gating: A principal energy transfer mechanism for mechanosensitive channels. Protein Sci 2016; 25:1954-1964. [PMID: 27530280 DOI: 10.1002/pro.3017] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 08/10/2016] [Indexed: 12/17/2022]
Abstract
Mechanosensitive (MS) channels are evolutionarily conserved membrane proteins that play essential roles in multiple cellular processes, including sensing mechanical forces and regulating osmotic pressure. Bacterial MscL and MscS are two prototypes of MS channels. Numerous structural studies, in combination with biochemical and cellular data, provide valuable insights into the mechanism of energy transfer from membrane tension to gating of the channel. We discuss these data in a unified two-state model of thermodynamics. In addition, we propose a lipid diffusion-mediated mechanism to explain the adaptation phenomenon of MscS.
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Affiliation(s)
- Xuejun C Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics Chinese Academy of Sciences, CAS Center for Excellence in Biomacromolecules, Beijing, 100101, China.
| | - Zhenfeng Liu
- National Laboratory of Biomacromolecules, Institute of Biophysics Chinese Academy of Sciences, CAS Center for Excellence in Biomacromolecules, Beijing, 100101, China
| | - Jie Li
- National Laboratory of Biomacromolecules, Institute of Biophysics Chinese Academy of Sciences, CAS Center for Excellence in Biomacromolecules, Beijing, 100101, China
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17
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Vickery ON, Machtens JP, Tamburrino G, Seeliger D, Zachariae U. Structural Mechanisms of Voltage Sensing in G Protein-Coupled Receptors. Structure 2016; 24:997-1007. [PMID: 27210286 PMCID: PMC4906246 DOI: 10.1016/j.str.2016.04.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 03/31/2016] [Accepted: 04/04/2016] [Indexed: 12/01/2022]
Abstract
G-protein-coupled receptors (GPCRs) form the largest superfamily of membrane proteins and one-third of all drug targets in humans. A number of recent studies have reported evidence for substantial voltage regulation of GPCRs. However, the structural basis of GPCR voltage sensing has remained enigmatic. Here, we present atomistic simulations on the δ-opioid and M2 muscarinic receptors, which suggest a structural and mechanistic explanation for the observed voltage-induced functional effects. The simulations reveal that the position of an internal Na(+) ion, recently detected to bind to a highly conserved aqueous pocket in receptor crystal structures, strongly responds to voltage changes. The movements give rise to gating charges in excellent agreement with previous experimental recordings. Furthermore, free energy calculations show that these rearrangements of Na(+) can be induced by physiological membrane voltages. Due to its role in receptor function and signal bias, the repositioning of Na(+) has important general implications for signal transduction in GPCRs.
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MESH Headings
- Animals
- Crystallography, X-Ray
- Humans
- Ion Channel Gating
- Models, Molecular
- Molecular Dynamics Simulation
- Protein Binding
- Protein Structure, Secondary
- Receptor, Muscarinic M2/chemistry
- Receptor, Muscarinic M2/metabolism
- Receptors, G-Protein-Coupled/chemistry
- Receptors, G-Protein-Coupled/metabolism
- Receptors, Opioid, delta/chemistry
- Receptors, Opioid, delta/metabolism
- Sodium/metabolism
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Affiliation(s)
- Owen N Vickery
- Computational Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK; Physics, School of Science and Engineering, University of Dundee, Nethergate, Dundee DD1 4NH, UK
| | - Jan-Philipp Machtens
- Forschungszentrum Jülich GmbH, Institute of Complex Systems, Zelluläre Biophysik (ICS-4), Leo-Brandt-Strasse, 52428 Jülich, Germany
| | - Giulia Tamburrino
- Computational Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK; Physics, School of Science and Engineering, University of Dundee, Nethergate, Dundee DD1 4NH, UK
| | - Daniel Seeliger
- Lead Identification and Optimization Support, Boehringer Ingelheim Pharma GmbH & Co KG, 88397 Biberach an der Riss, Germany
| | - Ulrich Zachariae
- Computational Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK; Physics, School of Science and Engineering, University of Dundee, Nethergate, Dundee DD1 4NH, UK.
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18
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Zhang XC, Zhou Y, Cao C. Thermodynamics of GPCR activation. BIOPHYSICS REPORTS 2016; 1:115-119. [PMID: 27340689 PMCID: PMC4871901 DOI: 10.1007/s41048-016-0017-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 01/06/2016] [Indexed: 12/30/2022] Open
Affiliation(s)
- Xuejun C Zhang
- National Laboratory of Macromolecules, National Center of Protein Science-Beijing, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Ye Zhou
- National Laboratory of Macromolecules, National Center of Protein Science-Beijing, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Can Cao
- National Laboratory of Macromolecules, National Center of Protein Science-Beijing, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
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19
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Zhang XC, Liu M, Zhao Y. How does transmembrane electrochemical potential drive the rotation of Fo motor in an ATP synthase? Protein Cell 2015; 6:784-91. [PMID: 26472431 PMCID: PMC4624678 DOI: 10.1007/s13238-015-0217-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
While the field of ATP synthase research has a long history filled with landmark discoveries, recent structural works provide us with important insights into the mechanisms that links the proton movement with the rotation of the Fo motor. Here, we propose a mechanism of unidirectional rotation of the Fo complex, which is in agreement with these new structural insights as well as our more general ΔΨ-driving hypothesis of membrane proteins: A proton path in the rotor-stator interface is formed dynamically in concert with the rotation of the Fo rotor. The trajectory of the proton viewed in the reference system of the rotor (R-path) must lag behind that of the stator (S-path). The proton moves from a higher energy site to a lower site following both trajectories simultaneously. The two trajectories meet each other at the transient proton-binding site, resulting in a relative rotation between the rotor and stator. The kinetic energy of protons gained from ΔΨ is transferred to the c-ring as the protons are captured sequentially by the binding sites along the proton path, thus driving the unidirectional rotation of the c-ring. Our ΔΨ-driving hypothesis on Fo motor is an attempt to unveil the robust mechanism of energy conversion in the highly conserved, ubiquitously expressed rotary ATP synthases.
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Affiliation(s)
- Xuejun C. Zhang
- National Laboratory of Macromolecules, National Center of Protein Science-Beijing, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Min Liu
- National Laboratory of Macromolecules, National Center of Protein Science-Beijing, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Yan Zhao
- National Laboratory of Macromolecules, National Center of Protein Science-Beijing, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
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20
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Zhang XC, Han L, Zhao Y. Thermodynamics of ABC transporters. Protein Cell 2015; 7:17-27. [PMID: 26408021 PMCID: PMC4707154 DOI: 10.1007/s13238-015-0211-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 08/11/2015] [Indexed: 01/09/2023] Open
Abstract
ABC transporters form the largest of all transporter families, and their structural study has made tremendous progress over recent years. However, despite such advances, the precise mechanisms that determine the energy-coupling between ATP hydrolysis and the conformational changes following substrate binding remain to be elucidated. Here, we present our thermodynamic analysis for both ABC importers and exporters, and introduce the two new concepts of differential-binding energy and elastic conformational energy into the discussion. We hope that the structural analysis of ABC transporters will henceforth take thermodynamic aspects of transport mechanisms into account as well.
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Affiliation(s)
- Xuejun C Zhang
- National Laboratory of Macromolecules, National Center of Protein Science-Beijing, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Lei Han
- National Laboratory of Macromolecules, National Center of Protein Science-Beijing, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yan Zhao
- National Laboratory of Macromolecules, National Center of Protein Science-Beijing, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
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