1
|
Ahn SY, Lee SJ, Yoon SI. Structural and biochemical analysis of the unique interactions of the Campylobacter jejuni CorA channel protein with divalent cations. Biochem Biophys Res Commun 2024; 723:150166. [PMID: 38810321 DOI: 10.1016/j.bbrc.2024.150166] [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: 05/17/2024] [Accepted: 05/22/2024] [Indexed: 05/31/2024]
Abstract
CorA is a Mg2+ channel that plays a key role in the homeostasis of intracellular Mg2+ in bacteria and archaea. CorA consists of a cytoplasmic domain and a transmembrane domain and generates a Mg2+ pathway by forming a pentamer in the cell membrane. CorA gating is regulated via negative feedback by Mg2+, which is accommodated by the pentamerization interface of the CorA cytoplasmic domain (CorACD). The Mg2+-binding sites of CorACD differ depending on the species, suggesting that the Mg2+-binding modes and Mg2+-mediated gating mechanisms of CorA vary across prokaryotes. To define the Mg2+-binding mechanism of CorA in the Campylobacter jejuni pathogen, we structurally and biochemically characterized C. jejuni CorACD (cjCorACD). cjCorACD adopts a three-layered α/β/α structure as observed in other CorA orthologs. Interestingly, cjCorACD exhibited enhanced thermostability in the presence of Ca2+, Ni2+, Zn2+, or Mn2+ in addition to Mg2+, indicating that cjCorACD interacts with diverse divalent cations. This cjCorACD stabilization is mediated by divalent cation accommodation by negatively charged residues located at the bottom of the cjCorACD structure away from the pentamerization interface. Consistently, cjCorACD exists as a monomer irrespective of the presence of divalent cations. We concluded that cjCorACD binds divalent cations in a unique pentamerization-independent manner.
Collapse
Affiliation(s)
- Si Yeon Ahn
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Su-Jin Lee
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Sung-Il Yoon
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Republic of Korea.
| |
Collapse
|
2
|
Uthayabalan S, Lake T, Stathopulos PB. MRS2 missense variation at Asp216 abrogates inhibitory Mg 2+ binding, potentiating cell migration and apoptosis resistance. Protein Sci 2024; 33:e5108. [PMID: 38989547 PMCID: PMC11237551 DOI: 10.1002/pro.5108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 06/06/2024] [Accepted: 06/24/2024] [Indexed: 07/12/2024]
Abstract
Mitochondrial magnesium (Mg2+) is a crucial modulator of protein stability, enzymatic activity, ATP synthesis, and cell death. Mitochondrial RNA splicing protein 2 (MRS2) is the main Mg2+ channel in the inner mitochondrial membrane that mediates influx into the matrix. Recent cryo-electron microscopy (cryo-EM) human MRS2 structures exhibit minimal conformational changes at high and low Mg2+, yet the regulation of human MRS2 and orthologues by Mg2+ binding to analogous matrix domains has been well established. Further, a missense variation at D216 has been identified associated with malignant melanoma and MRS2 expression and activity is implicated in gastric cancer. Thus, to gain more mechanistic and functional insight into Mg2+ sensing by the human MRS2 matrix domain and the association with proliferative disease, we assessed the structural, biophysical, and functional effects of a D216Q mutant. We show that the D216Q mutation is sufficient to abrogate Mg2+-binding and associated conformational changes including increased α-helicity, stability, and monomerization. Further, we reveal that the MRS2 matrix domains interact with ~μM affinity, which is weakened by up to two orders of magnitude in the presence of Mg2+ for wild-type but unaffected for D216Q. Finally, we demonstrate the importance of Mg2+ sensing by MRS2 to prevent matrix Mg2+ overload as HeLa cells overexpressing MRS2 show enhanced Mg2+ uptake, cell migration, and resistance to apoptosis while MRS2 D216Q robustly potentiates these cancer phenotypes. Collectively, our findings further define the MRS2 matrix domain as a critical Mg2+ sensor that undergoes conformational and assembly changes upon Mg2+ interactions dependent on D216 to temper matrix Mg2+ overload.
Collapse
Affiliation(s)
- Sukanthathulse Uthayabalan
- Department of Physiology and Pharmacology, Schulich School of Medicine and DentistryUniversity of Western OntarioLondonOntarioCanada
| | - Taylor Lake
- Department of Physiology and Pharmacology, Schulich School of Medicine and DentistryUniversity of Western OntarioLondonOntarioCanada
| | - Peter B. Stathopulos
- Department of Physiology and Pharmacology, Schulich School of Medicine and DentistryUniversity of Western OntarioLondonOntarioCanada
| |
Collapse
|
3
|
Lai LTF, Balaraman J, Zhou F, Matthies D. Cryo-EM structures of human magnesium channel MRS2 reveal gating and regulatory mechanisms. Nat Commun 2023; 14:7207. [PMID: 37938562 PMCID: PMC10632456 DOI: 10.1038/s41467-023-42599-3] [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: 08/22/2023] [Accepted: 10/16/2023] [Indexed: 11/09/2023] Open
Abstract
Magnesium ions (Mg2+) play an essential role in cellular physiology. In mitochondria, protein and ATP synthesis and various metabolic pathways are directly regulated by Mg2+. MRS2, a magnesium channel located in the inner mitochondrial membrane, mediates the influx of Mg2+ into the mitochondrial matrix and regulates Mg2+ homeostasis. Knockdown of MRS2 in human cells leads to reduced uptake of Mg2+ into mitochondria and disruption of the mitochondrial metabolism. Despite the importance of MRS2, the Mg2+ translocation and regulation mechanisms of MRS2 are still unclear. Here, using cryo-EM we report the structures of human MRS2 in the presence and absence of Mg2+ at 2.8 Å and 3.3 Å, respectively. From the homo-pentameric structures, we identify R332 and M336 as major gating residues, which are then tested using mutagenesis and two cellular divalent ion uptake assays. A network of hydrogen bonds is found connecting the gating residue R332 to the soluble domain, potentially regulating the gate. Two Mg2+-binding sites are identified in the MRS2 soluble domain, distinct from the two sites previously reported in CorA, a homolog of MRS2 in prokaryotes. Altogether, this study provides the molecular basis for understanding the Mg2+ translocation and regulatory mechanisms of MRS2.
Collapse
Affiliation(s)
- Louis Tung Faat Lai
- Unit on Structural Biology, Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jayashree Balaraman
- Unit on Structural Biology, Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Fei Zhou
- Unit on Structural Biology, Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Doreen Matthies
- Unit on Structural Biology, Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA.
| |
Collapse
|
4
|
Lai LTF, Balaraman J, Zhou F, Matthies D. Cryo-EM structures of human magnesium channel MRS2 reveal gating and regulatory mechanisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.22.553867. [PMID: 37662257 PMCID: PMC10473633 DOI: 10.1101/2023.08.22.553867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Magnesium ions (Mg2+) play an essential role in cellular physiology. In mitochondria, protein and ATP synthesis and various metabolic pathways are directly regulated by Mg2+. MRS2, a magnesium channel located in the inner mitochondrial membrane, mediates the influx of Mg2+ into the mitochondrial matrix and regulates Mg2+ homeostasis. Knockdown of MRS2 in human cells leads to reduced uptake of Mg2+ into mitochondria and disruption of the mitochondrial metabolism. Despite the importance of MRS2, the Mg2+ translocation and regulation mechanisms of MRS2 are still unclear. Here, using cryo-EM we determined the structure of human MRS2 in the presence and absence of Mg2+ at 2.8 Å and 3.3 Å, respectively. From the homo-pentameric structures, we identified R332 and M336 as major gating residues, which were then tested using mutagenesis and two cellular divalent ion uptake assays. A network of hydrogen bonds was found connecting the gating residue R332 to the soluble domain, potentially regulating the gate. Two Mg2+-binding sites were identified in the MRS2 soluble domain, distinct from the two sites previously reported in CorA, a homolog of MRS2 in prokaryotes. Altogether, this study provides the molecular basis for understanding the Mg2+ translocation and regulatory mechanisms of MRS2.
Collapse
Affiliation(s)
- Louis Tung Faat Lai
- Unit on Structural Biology, Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda MD 20892, USA
| | - Jayashree Balaraman
- Unit on Structural Biology, Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda MD 20892, USA
| | - Fei Zhou
- Unit on Structural Biology, Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda MD 20892, USA
| | - Doreen Matthies
- Unit on Structural Biology, Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda MD 20892, USA
| |
Collapse
|
5
|
Li M, Li Y, Lu Y, Li J, Lu X, Ren Y, Wen T, Wang Y, Chang S, Zhang X, Yang X, Shen Y. Molecular basis of Mg 2+ permeation through the human mitochondrial Mrs2 channel. Nat Commun 2023; 14:4713. [PMID: 37543649 PMCID: PMC10404273 DOI: 10.1038/s41467-023-40516-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 07/25/2023] [Indexed: 08/07/2023] Open
Abstract
Mitochondrial RNA splicing 2 (Mrs2), a eukaryotic CorA ortholog, enables Mg2+ to permeate the inner mitochondrial membrane and plays an important role in mitochondrial metabolic function. However, the mechanism by which Mrs2 permeates Mg2+ remains unclear. Here, we report four cryo-electron microscopy (cryo-EM) reconstructions of Homo sapiens Mrs2 (hMrs2) under various conditions. All of these hMrs2 structures form symmetrical pentamers with very similar pentamer and protomer conformations. A special structural feature of Cl--bound R-ring, which consists of five Arg332 residues, was found in the hMrs2 structure. Molecular dynamics simulations and mitochondrial Mg2+ uptake assays show that the R-ring may function as a charge repulsion barrier, and Cl- may function as a ferry to jointly gate Mg2+ permeation in hMrs2. In addition, the membrane potential is likely to be the driving force for Mg2+ permeation. Our results provide insights into the channel assembly and Mg2+ permeation of hMrs2.
Collapse
Affiliation(s)
- Ming Li
- State Key Laboratory of Medicinal Chemical Biology and Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin, 300350, China
| | - Yang Li
- State Key Laboratory of Medicinal Chemical Biology and Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin, 300350, China
| | - Yue Lu
- State Key Laboratory of Medicinal Chemical Biology and Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin, 300350, China
| | - Jianhui Li
- State Key Laboratory of Medicinal Chemical Biology and Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin, 300350, China
| | - Xuhang Lu
- State Key Laboratory of Medicinal Chemical Biology and Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin, 300350, China
| | - Yue Ren
- State Key Laboratory of Medicinal Chemical Biology and Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin, 300350, China
| | - Tianlei Wen
- State Key Laboratory of Medicinal Chemical Biology and Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin, 300350, China
| | - Yaojie Wang
- State Key Laboratory of Medicinal Chemical Biology and Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin, 300350, China
| | - Shenghai Chang
- Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310058, China
- Center of Cryo Electron Microscopy, Zhejiang University, Hangzhou, 310058, China
| | - Xing Zhang
- Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310058, China
- Center of Cryo Electron Microscopy, Zhejiang University, Hangzhou, 310058, China
| | - Xue Yang
- State Key Laboratory of Medicinal Chemical Biology and Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin, 300350, China.
| | - Yuequan Shen
- State Key Laboratory of Medicinal Chemical Biology and Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin, 300350, China.
| |
Collapse
|
6
|
Aoki K, Yamamoto K, Ohkuma M, Sugita T, Tanaka N, Takashima M. Hyphal Growth in Trichosporon asahii Is Accelerated by the Addition of Magnesium. Microbiol Spectr 2023; 11:e0424222. [PMID: 37102973 PMCID: PMC10269644 DOI: 10.1128/spectrum.04242-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 04/10/2023] [Indexed: 04/28/2023] Open
Abstract
Fungal dimorphism involves two morphologies: a unicellular yeast cell and a multicellular hyphal form. Invasion of hyphae into human cells causes severe opportunistic infections. The transition between yeast and hyphal forms is associated with the virulence of fungi; however, the mechanism is poorly understood. Therefore, we aimed to identify factors that induce hyphal growth of Trichosporon asahii, a dimorphic basidiomycete that causes trichosporonosis. T. asahii showed poor growth and formed small cells containing large lipid droplets and fragmented mitochondria when cultivated for 16 h in a nutrient-deficient liquid medium. However, these phenotypes were suppressed via the addition of yeast nitrogen base. When T. asahii cells were cultivated in the presence of different compounds present in the yeast nitrogen base, we found that magnesium sulfate was a key factor for inducing cell elongation, and its addition dramatically restored hyphal growth in T. asahii. In T. asahii hyphae, vacuoles were enlarged, the size of lipid droplets was decreased, and mitochondria were distributed throughout the cell cytoplasm and adjacent to the cell walls. Additionally, hyphal growth was disrupted due to treatment with an actin inhibitor. The actin inhibitor latrunculin A disrupted the mitochondrial distribution even in hyphal cells. Furthermore, magnesium sulfate treatment accelerated hyphal growth in T. asahii for 72 h when the cells were cultivated in a nutrient-deficient liquid medium. Collectively, our results suggest that an increase in magnesium levels triggers the transition from the yeast to hyphal form in T. asahii. These findings will support studies on the pathogenesis of fungi and aid in developing treatments. IMPORTANCE Understanding the mechanism underlying fungal dimorphism is crucial to discern its invasion into human cells. Invasion is caused by the hyphal form rather than the yeast form; therefore, it is important to understand the mechanism of transition from the yeast to hyphal form. To study the transition mechanism, we utilized Trichosporon asahii, a dimorphic basidiomycete that causes severe trichosporonosis since there are fewer studies on T. asahii than on ascomycetes. This study suggests that an increase in Mg2+, the most abundant mineral in living cells, triggers growth of filamentous hyphae and increases the distribution of mitochondria throughout the cell cytoplasm and adjacent to the cell walls in T. asahii. Understanding the mechanism of hyphal growth triggered by Mg2+ increase will provide a model system to explore fungal pathogenicity in the future.
Collapse
Affiliation(s)
- Keita Aoki
- Laboratory of Yeast Systematics, Tokyo NODAI Research Institute, Tokyo University of Agriculture, Setagaya, Tokyo, Japan
| | - Kosuke Yamamoto
- Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture, Setagaya, Tokyo, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
| | - Takashi Sugita
- Department of Microbiology, Meiji Pharmaceutical University, Kiyose, Tokyo, Japan
| | - Naoto Tanaka
- Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture, Setagaya, Tokyo, Japan
| | - Masako Takashima
- Laboratory of Yeast Systematics, Tokyo NODAI Research Institute, Tokyo University of Agriculture, Setagaya, Tokyo, Japan
| |
Collapse
|
7
|
Uthayabalan S, Vishnu N, Madesh M, Stathopulos PB. The human MRS2 magnesium-binding domain is a regulatory feedback switch for channel activity. Life Sci Alliance 2023; 6:e202201742. [PMID: 36754568 PMCID: PMC9909464 DOI: 10.26508/lsa.202201742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 01/25/2023] [Accepted: 01/26/2023] [Indexed: 02/10/2023] Open
Abstract
Mitochondrial RNA splicing 2 (MRS2) forms a magnesium (Mg2+) entry protein channel in mitochondria. Whereas MRS2 contains two transmembrane domains constituting a pore on the inner mitochondrial membrane, most of the protein resides within the matrix. Yet, the precise structural and functional role of this obtrusive amino terminal domain (NTD) in human MRS2 is unknown. Here, we show that the MRS2 NTD self-associates into a homodimer, contrasting the pentameric assembly of CorA, an orthologous bacterial channel. Mg2+ and calcium suppress lower and higher order oligomerization of MRS2 NTD, whereas cobalt has no effect on the NTD but disassembles full-length MRS2. Mutating-pinpointed residues-mediating Mg2+ binding to the NTD not only selectively decreases Mg2+-binding affinity ∼sevenfold but also abrogates Mg2+ binding-induced secondary, tertiary, and quaternary structure changes. Disruption of NTD Mg2+ binding strikingly potentiates mitochondrial Mg2+ uptake in WT and Mrs2 knockout cells. Our work exposes a mechanism for human MRS2 autoregulation by negative feedback from the NTD and identifies a novel gain of function mutant with broad applicability to future Mg2+ signaling research.
Collapse
Affiliation(s)
- Sukanthathulse Uthayabalan
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Canada
| | - Neelanjan Vishnu
- Center for Mitochondrial Medicine, Department of Medicine, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Muniswamy Madesh
- Center for Mitochondrial Medicine, Department of Medicine, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Peter B Stathopulos
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Canada
| |
Collapse
|
8
|
Wei S, Thakur N, Ray AP, Jin B, Obeng S, McCurdy CR, McMahon LR, Gutiérrez-de-Terán H, Eddy MT, Lamichhane R. Slow conformational dynamics of the human A 2A adenosine receptor are temporally ordered. Structure 2022; 30:329-337.e5. [PMID: 34895472 PMCID: PMC8897252 DOI: 10.1016/j.str.2021.11.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 09/26/2021] [Accepted: 11/17/2021] [Indexed: 01/12/2023]
Abstract
A more complete depiction of protein energy landscapes includes the identification of different function-related conformational states and the determination of the pathways connecting them. We used total internal reflection fluorescence (TIRF) imaging to investigate the conformational dynamics of the human A2A adenosine receptor (A2AAR), a class A G protein-coupled receptor (GPCR), at the single-molecule level. Slow, reversible conformational exchange was observed among three different fluorescence emission states populated for agonist-bound A2AAR. Transitions among these states predominantly occurred in a specific order, and exchange between inactive and active-like conformations proceeded through an intermediate state. Models derived from molecular dynamics simulations with available A2AAR structures rationalized the relative fluorescence emission intensities for the highest and lowest emission states but not the transition state. This suggests that the functionally critical intermediate state required to achieve activation is not currently visualized among available A2AAR structures.
Collapse
Affiliation(s)
- Shushu Wei
- Department of Biochemistry & Cellular and Molecular Biology, College of Arts and Sciences, University of Tennessee, 1311 Cumberland Avenue, Knoxville, TN 37932, USA
| | - Naveen Thakur
- Department of Chemistry, College of Liberal Arts and Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | - Arka P Ray
- Department of Chemistry, College of Liberal Arts and Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | - Beining Jin
- Department of Chemistry, College of Liberal Arts and Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | - Samuel Obeng
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA; Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA
| | - Christopher R McCurdy
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA; Translational Drug Development Core, Clinical and Translational Sciences Institute, University of Florida, Gainesville, FL 32610, USA
| | - Lance R McMahon
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA
| | - Hugo Gutiérrez-de-Terán
- Department of Cell and Molecular Biology, Uppsala University, B.M.C., Box 596, Uppsala 751 24, Sweden
| | - Matthew T Eddy
- Department of Chemistry, College of Liberal Arts and Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA.
| | - Rajan Lamichhane
- Department of Biochemistry & Cellular and Molecular Biology, College of Arts and Sciences, University of Tennessee, 1311 Cumberland Avenue, Knoxville, TN 37932, USA.
| |
Collapse
|
9
|
Johansen NT, Bonaccorsi M, Bengtsen T, Larsen AH, Tidemand FG, Pedersen MC, Huda P, Berndtsson J, Darwish T, Yepuri NR, Martel A, Pomorski TG, Bertarello A, Sansom MS, Rapp M, Crehuet R, Schubeis T, Lindorff-Larsen K, Pintacuda G, Arleth L. Mg 2+-dependent conformational equilibria in CorA and an integrated view on transport regulation. eLife 2022; 11:71887. [PMID: 35129435 PMCID: PMC8865849 DOI: 10.7554/elife.71887] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 02/04/2022] [Indexed: 11/13/2022] Open
Abstract
The CorA family of proteins regulates the homeostasis of divalent metal ions in many bacteria, archaea, and eukaryotic mitochondria, making it an important target in the investigation of the mechanisms of transport and its functional regulation. Although numerous structures of open and closed channels are now available for the CorA family, the mechanism of the transport regulation remains elusive. Here, we investigated the conformational distribution and associated dynamic behaviour of the pentameric Mg2+ channel CorA at room temperature using small-angle neutron scattering (SANS) in combination with molecular dynamics (MD) simulations and solid-state nuclear magnetic resonance spectroscopy (NMR). We find that neither the Mg2+-bound closed structure nor the Mg2+-free open forms are sufficient to explain the average conformation of CorA. Our data support the presence of conformational equilibria between multiple states, and we further find a variation in the behaviour of the backbone dynamics with and without Mg2+. We propose that CorA must be in a dynamic equilibrium between different non-conducting states, both symmetric and asymmetric, regardless of bound Mg2+ but that conducting states become more populated in Mg2+-free conditions. These properties are regulated by backbone dynamics and are key to understanding the functional regulation of CorA.
Collapse
Affiliation(s)
| | - Marta Bonaccorsi
- Centre de RMN à Très hauts Champs de Lyon, UMR 5280, CNRS, University of Lyon, Villeurbanne, France
| | - Tone Bengtsen
- Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Andreas Haahr Larsen
- Condensed Matter Physics, Niels Bohr Institute, University of Copenhagen, Copenhagen E, Denmark
| | | | - Martin Cramer Pedersen
- Condensed Matter Physics, Niels Bohr Institute, University of Copenhagen, Copenhagen E, Denmark
| | - Pie Huda
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, Australia
| | - Jens Berndtsson
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Tamim Darwish
- National Deuteration Facility, Australian Nuclear Science and Technology Organization, Lucas Heights, Australia
| | - Nageshewar Rao Yepuri
- National Deuteration Facility, Australian Nuclear Science and Technology Organization, Lucas Heights, Australia
| | | | - Thomas Günther Pomorski
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Andrea Bertarello
- Centre de RMN à Très hauts Champs de Lyon, UMR 5280, CNRS, University of Lyon, Villeurbanne, France
| | - Mark Sp Sansom
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Mikaela Rapp
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Ramon Crehuet
- Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Tobias Schubeis
- Centre de RMN à Très hauts Champs de Lyon, UMR 5280, CNRS, University of Lyon, Villeurbanne, France
| | | | - Guido Pintacuda
- Centre de RMN à Très hauts Champs de Lyon, UMR 5280, CNRS, University of Lyon, Villeurbanne, France
| | - Lise Arleth
- Condensed Matter Physics, Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
10
|
Kapla J, Rodríguez-Espigares I, Ballante F, Selent J, Carlsson J. Can molecular dynamics simulations improve the structural accuracy and virtual screening performance of GPCR models? PLoS Comput Biol 2021; 17:e1008936. [PMID: 33983933 PMCID: PMC8186765 DOI: 10.1371/journal.pcbi.1008936] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 06/08/2021] [Accepted: 04/02/2021] [Indexed: 01/14/2023] Open
Abstract
The determination of G protein-coupled receptor (GPCR) structures at atomic resolution has improved understanding of cellular signaling and will accelerate the development of new drug candidates. However, experimental structures still remain unavailable for a majority of the GPCR family. GPCR structures and their interactions with ligands can also be modelled computationally, but such predictions have limited accuracy. In this work, we explored if molecular dynamics (MD) simulations could be used to refine the accuracy of in silico models of receptor-ligand complexes that were submitted to a community-wide assessment of GPCR structure prediction (GPCR Dock). Two simulation protocols were used to refine 30 models of the D3 dopamine receptor (D3R) in complex with an antagonist. Close to 60 μs of simulation time was generated and the resulting MD refined models were compared to a D3R crystal structure. In the MD simulations, the receptor models generally drifted further away from the crystal structure conformation. However, MD refinement was able to improve the accuracy of the ligand binding mode. The best refinement protocol improved agreement with the experimentally observed ligand binding mode for a majority of the models. Receptor structures with improved virtual screening performance, which was assessed by molecular docking of ligands and decoys, could also be identified among the MD refined models. Application of weak restraints to the transmembrane helixes in the MD simulations further improved predictions of the ligand binding mode and second extracellular loop. These results provide guidelines for application of MD refinement in prediction of GPCR-ligand complexes and directions for further method development.
Collapse
Affiliation(s)
- Jon Kapla
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Ismael Rodríguez-Espigares
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences of Pompeu Fabra University (UPF), Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Flavio Ballante
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Jana Selent
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences of Pompeu Fabra University (UPF), Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Jens Carlsson
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| |
Collapse
|
11
|
Nemchinova M, Melcr J, Wassenaar TA, Marrink SJ, Guskov A. Asymmetric CorA Gating Mechanism as Observed by Molecular Dynamics Simulations. J Chem Inf Model 2021; 61:2407-2417. [PMID: 33886304 PMCID: PMC8154316 DOI: 10.1021/acs.jcim.1c00261] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
The CorA family of
proteins plays a housekeeping role in the homeostasis
of divalent metal ions in many bacteria and archaea as well as in
mitochondria of eukaryotes, rendering it an important target to study
the mechanisms of divalent transport and regulation across different
life domains. Despite numerous studies, the mechanistic details of
the channel gating and the transport of the metal ions are still not
entirely understood. Here, we use all-atom and coarse-grained molecular
dynamics simulations combined with in vitro experiments
to investigate the influence of divalent cations on the function of
CorA. Simulations reveal pronounced asymmetric movements of monomers
that enable the rotation of the α7 helix and the cytoplasmic
subdomain with the subsequent formation of new interactions and the
opening of the channel. These computational results are functionally
validated using site-directed mutagenesis of the intracellular cytoplasmic
domain residues and biochemical assays. The obtained results infer
a complex network of interactions altering the structure of CorA to
allow gating. Furthermore, we attempt to reconcile the existing gating
hypotheses for CorA to conclude the mechanism of transport of divalent
cations via these proteins.
Collapse
Affiliation(s)
- Mariia Nemchinova
- Groningen Institute for Biomolecular Sciences and Biotechnology, University of Groningen, 9747AG Groningen, The Netherlands
| | - Josef Melcr
- Groningen Institute for Biomolecular Sciences and Biotechnology, University of Groningen, 9747AG Groningen, The Netherlands
| | - Tsjerk A Wassenaar
- Groningen Institute for Biomolecular Sciences and Biotechnology, University of Groningen, 9747AG Groningen, The Netherlands
| | - Siewert J Marrink
- Groningen Institute for Biomolecular Sciences and Biotechnology, University of Groningen, 9747AG Groningen, The Netherlands
| | - Albert Guskov
- Groningen Institute for Biomolecular Sciences and Biotechnology, University of Groningen, 9747AG Groningen, The Netherlands
| |
Collapse
|
12
|
Azulay H, Pellach Leshem M, Qvit N. An Approach to comparing protein structures and origami models - Part 2. Multi-domain proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183411. [PMID: 32710853 DOI: 10.1016/j.bbamem.2020.183411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 07/10/2020] [Accepted: 07/17/2020] [Indexed: 11/29/2022]
Abstract
Protein structure is an important field of research, with particular significance in its potential applications in biomedicine and nanotechnology. In a recent study, we presented a general approach for comparing protein structures and origami models and demonstrated it with single-domain proteins. For example, the analysis of the α-helical barrel of the outer membrane protein A (OmpA) suggests that there are similar patterns between its structure and the Kresling origami model, providing insight into structure-activity relationships. Here we demonstrate that our approach can be expanded beyond single-domain proteins to also include multi-domain proteins, and to study dynamic processes of biomolecules. Two examples are given: (1) The eukaryotic chaperonin (TRiC) protein is compared with a newly generated origami model, and with an origami model that is constructed from two copies of the Flasher origami model, and (2) the CorA Magnesium transport system is compared with a newly generated origami model and with an origami model that combines the Kresling and Flasher origami models. Based on the analysis of the analog origami models, it is indicated that it is possible to identify building blocks for constructing assembled origami models that are analogous to protein structures. In addition, it is identified that the expansion/collapse mechanisms of the TRiC and CorA are auxetic. Namely, these proteins require a single motion for synchronized folding along two or three axes.
Collapse
Affiliation(s)
| | - Michal Pellach Leshem
- The Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Henrietta Szold St. 8, POB 1589, Safed, Israel
| | - Nir Qvit
- The Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Henrietta Szold St. 8, POB 1589, Safed, Israel.
| |
Collapse
|
13
|
Biophysical Insight on the Membrane Insertion of an Arginine-Rich Cell-Penetrating Peptide. Int J Mol Sci 2019; 20:ijms20184441. [PMID: 31505894 PMCID: PMC6769507 DOI: 10.3390/ijms20184441] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 08/30/2019] [Accepted: 09/04/2019] [Indexed: 12/21/2022] Open
Abstract
Cell-penetrating peptides (CPPs) are short peptides that can translocate and transport cargoes into the intracellular milieu by crossing biological membranes. The mode of interaction and internalization of cell-penetrating peptides has long been controversial. While their interaction with anionic membranes is quite well understood, the insertion and behavior of CPPs in zwitterionic membranes, a major lipid component of eukaryotic cell membranes, is poorly studied. Herein, we investigated the membrane insertion of RW16 into zwitterionic membranes, a versatile CPP that also presents antibacterial and antitumor activities. Using complementary approaches, including NMR spectroscopy, fluorescence spectroscopy, circular dichroism, and molecular dynamic simulations, we determined the high-resolution structure of RW16 and measured its membrane insertion and orientation properties into zwitterionic membranes. Altogether, these results contribute to explaining the versatile properties of this peptide toward zwitterionic lipids.
Collapse
|
14
|
Igaev M, Kutzner C, Bock LV, Vaiana AC, Grubmüller H. Automated cryo-EM structure refinement using correlation-driven molecular dynamics. eLife 2019; 8:e43542. [PMID: 30829573 PMCID: PMC6424565 DOI: 10.7554/elife.43542] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 03/03/2019] [Indexed: 12/22/2022] Open
Abstract
We present a correlation-driven molecular dynamics (CDMD) method for automated refinement of atomistic models into cryo-electron microscopy (cryo-EM) maps at resolutions ranging from near-atomic to subnanometer. It utilizes a chemically accurate force field and thermodynamic sampling to improve the real-space correlation between the modeled structure and the cryo-EM map. Our framework employs a gradual increase in resolution and map-model agreement as well as simulated annealing, and allows fully automated refinement without manual intervention or any additional rotamer- and backbone-specific restraints. Using multiple challenging systems covering a wide range of map resolutions, system sizes, starting model geometries and distances from the target state, we assess the quality of generated models in terms of both model accuracy and potential of overfitting. To provide an objective comparison, we apply several well-established methods across all examples and demonstrate that CDMD performs best in most cases.
Collapse
Affiliation(s)
- Maxim Igaev
- Department of Theoretical and Computational BiophysicsMax Planck Institute for Biophysical ChemistryGöttingenGermany
| | - Carsten Kutzner
- Department of Theoretical and Computational BiophysicsMax Planck Institute for Biophysical ChemistryGöttingenGermany
| | - Lars V Bock
- Department of Theoretical and Computational BiophysicsMax Planck Institute for Biophysical ChemistryGöttingenGermany
| | - Andrea C Vaiana
- Department of Theoretical and Computational BiophysicsMax Planck Institute for Biophysical ChemistryGöttingenGermany
| | - Helmut Grubmüller
- Department of Theoretical and Computational BiophysicsMax Planck Institute for Biophysical ChemistryGöttingenGermany
| |
Collapse
|
15
|
Rangubpit W, Kitjaruwankul S, Boonamnaj P, Sompornpisut P, Pandey R. Globular bundles and entangled network of proteins (CorA) by a coarse-grained Monte Carlo simulation. AIMS BIOPHYSICS 2019. [DOI: 10.3934/biophy.2019.2.68] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
16
|
Kawanabe A, Hashimoto M, Nishizawa M, Nishizawa K, Narita H, Yonezawa T, Jinno Y, Sakata S, Nakagawa A, Okamura Y. The hydrophobic nature of a novel membrane interface regulates the enzyme activity of a voltage-sensing phosphatase. eLife 2018; 7:41653. [PMID: 30484774 PMCID: PMC6298786 DOI: 10.7554/elife.41653] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 11/28/2018] [Indexed: 01/24/2023] Open
Abstract
Voltage-sensing phosphatases (VSP) contain a voltage sensor domain (VSD) similar to that of voltage-gated ion channels but lack a pore-gate domain. A VSD in a VSP regulates the cytoplasmic catalytic region (CCR). However, the mechanisms by which the VSD couples to the CCR remain elusive. Here we report a membrane interface (named ‘the hydrophobic spine’), which is essential for the coupling of the VSD and CCR. Our molecular dynamics simulations suggest that the hydrophobic spine of Ciona intestinalis VSP (Ci-VSP) provides a hinge-like motion for the CCR through the loose membrane association of the phosphatase domain. Electrophysiological experiments indicate that the voltage-dependent phosphatase activity of Ci-VSP depends on the hydrophobicity and presence of an aromatic ring in the hydrophobic spine. Analysis of conformational changes in the VSD and CCR suggests that the VSP has two states with distinct enzyme activities and that the second transition depends on the hydrophobic spine.
Collapse
Affiliation(s)
- Akira Kawanabe
- Integrative Physiology, Department of Physiology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Masaki Hashimoto
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | | | | | - Hirotaka Narita
- Institute for Protein Research, Osaka University, Osaka, Japan
| | - Tomoko Yonezawa
- Integrative Physiology, Department of Physiology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Yuka Jinno
- Integrative Physiology, Department of Physiology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Souhei Sakata
- Department of Physiology, Division of Life Sciences, Faculty of Medicine, Osaka Medical College, Osaka, Japan
| | | | - Yasushi Okamura
- Integrative Physiology, Department of Physiology, Graduate School of Medicine, Osaka University, Osaka, Japan.,Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| |
Collapse
|
17
|
Kowatz T, Maguire ME. Loss of cytosolic Mg 2+ binding sites in the Thermotoga maritima CorA Mg 2+ channel is not sufficient for channel opening. Biochim Biophys Acta Gen Subj 2018; 1863:25-30. [PMID: 30293964 DOI: 10.1016/j.bbagen.2018.09.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 08/29/2018] [Accepted: 09/03/2018] [Indexed: 10/28/2022]
Abstract
The CorA Mg2+ channel is a homopentamer with five-fold symmetry. Each monomer consists of a large cytoplasmic domain and two transmembrane helices connected via a short periplasmic loop. In the Thermotoga maritima CorA crystal structure, a Mg2+ is bound between D89 of one monomer and D253 of the adjacent monomer (M1 binding site). Release of Mg2+ from these sites has been hypothesized to cause opening of the channel. We generated mutants to disrupt Mg2+ interaction with the M1 site. Crystal structures of the D89K/D253K and D89R/D253R mutants, determined to 3.05 and 3.3 Å, respectively, showed no significant structural differences with the wild type structure despite absence of Mg2+ at the M1 sites. Both mutants still appear to be in the closed state. All three mutant CorA proteins exhibited transport of 63Ni2+, indicating functionality. Thus, absence of Mg2+ from the M1 sites neither causes channel opening nor prevents function. We also provide evidence that the T. maritima CorA is a Mg2+ channel and not a Co2+ channel.
Collapse
Affiliation(s)
- Thomas Kowatz
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106-4965, USA
| | - Michael E Maguire
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106-4965, USA.
| |
Collapse
|
18
|
Borroto-Escuela DO, Rodriguez D, Romero-Fernandez W, Kapla J, Jaiteh M, Ranganathan A, Lazarova T, Fuxe K, Carlsson J. Mapping the Interface of a GPCR Dimer: A Structural Model of the A 2A Adenosine and D 2 Dopamine Receptor Heteromer. Front Pharmacol 2018; 9:829. [PMID: 30214407 PMCID: PMC6125358 DOI: 10.3389/fphar.2018.00829] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 07/10/2018] [Indexed: 12/17/2022] Open
Abstract
The A2A adenosine (A2AR) and D2 dopamine (D2R) receptors form oligomers in the cell membrane and allosteric interactions across the A2AR–D2R heteromer represent a target for development of drugs against central nervous system disorders. However, understanding of the molecular determinants of A2AR–D2R heteromerization and the allosteric antagonistic interactions between the receptor protomers is still limited. In this work, a structural model of the A2AR–D2R heterodimer was generated using a combined experimental and computational approach. Regions involved in the heteromer interface were modeled based on the effects of peptides derived from the transmembrane (TM) helices on A2AR–D2R receptor–receptor interactions in bioluminescence resonance energy transfer (BRET) and proximity ligation assays. Peptides corresponding to TM-IV and TM-V of the A2AR blocked heterodimer interactions and disrupted the allosteric effect of A2AR activation on D2R agonist binding. Protein–protein docking was used to construct a model of the A2AR–D2R heterodimer with a TM-IV/V interface, which was refined using molecular dynamics simulations. Mutations in the predicted interface reduced A2AR–D2R interactions in BRET experiments and altered the allosteric modulation. The heterodimer model provided insights into the structural basis of allosteric modulation and the technique developed to characterize the A2AR–D2R interface can be extended to study the many other G protein-coupled receptors that engage in heteroreceptor complexes.
Collapse
Affiliation(s)
| | - David Rodriguez
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Wilber Romero-Fernandez
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Jon Kapla
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Mariama Jaiteh
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Anirudh Ranganathan
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Tzvetana Lazarova
- Department of Biochemistry and Molecular Biology, Institute of Neuroscience, Faculty of Medicine, Autonomous University of Barcelona, Barcelona, Spain
| | - Kjell Fuxe
- Department of Neuroscience, Karolinska Institute, Stockholm, Sweden
| | - Jens Carlsson
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| |
Collapse
|
19
|
Strakova K, Matricon P, Yokota C, Arthofer E, Bernatik O, Rodriguez D, Arenas E, Carlsson J, Bryja V, Schulte G. The tyrosine Y250 2.39 in Frizzled 4 defines a conserved motif important for structural integrity of the receptor and recruitment of Disheveled. Cell Signal 2017; 38:85-96. [DOI: 10.1016/j.cellsig.2017.06.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 06/09/2017] [Accepted: 06/26/2017] [Indexed: 12/16/2022]
|
20
|
Agonist-induced dimer dissociation as a macromolecular step in G protein-coupled receptor signaling. Nat Commun 2017; 8:226. [PMID: 28790300 PMCID: PMC5548745 DOI: 10.1038/s41467-017-00253-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 06/14/2017] [Indexed: 01/28/2023] Open
Abstract
G protein-coupled receptors (GPCRs) constitute the largest family of cell surface receptors. They can exist and act as dimers, but the requirement of dimers for agonist-induced signal initiation and structural dynamics remains largely unknown. Frizzled 6 (FZD6) is a member of Class F GPCRs, which bind WNT proteins to initiate signaling. Here, we show that FZD6 dimerizes and that the dimer interface of FZD6 is formed by the transmembrane α-helices four and five. Most importantly, we present the agonist-induced dissociation/re-association of a GPCR dimer through the use of live cell imaging techniques. Further analysis of a dimerization-impaired FZD6 mutant indicates that dimer dissociation is an integral part of FZD6 signaling to extracellular signal-regulated kinases1/2. The discovery of agonist-dependent dynamics of dimers as an intrinsic process of receptor activation extends our understanding of Class F and other dimerizing GPCRs, offering novel targets for dimer-interfering small molecules. Frizzled 6 (FZD6) is a G protein-coupled receptor (GPCR) involved in several cellular processes. Here, the authors use live cell imaging and spectroscopy to show that FZD6 forms dimers, whose association is regulated by WNT proteins and that dimer dissociation is crucial for FZD6 signaling.
Collapse
|
21
|
Kitjaruwankul S, Khrutto C, Sompornpisut P, Farmer BL, Pandey RB. Asymmetry in structural response of inner and outer transmembrane segments of CorA protein by a coarse-grain model. J Chem Phys 2016; 145:135101. [PMID: 27782431 DOI: 10.1063/1.4963807] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Structure of CorA protein and its inner (i.corA) and outer (o.corA) transmembrane (TM) components are investigated as a function of temperature by a coarse-grained Monte Carlo simulation. Thermal response of i.corA is found to differ considerably from that of the outer component, o.corA. Analysis of the radius of gyration reveals that the inner TM component undergoes a continuous transition from a globular conformation to a random coil structure on raising the temperature. In contrast, the outer transmembrane component exhibits an abrupt (nearly discontinuous) thermal response in a narrow range of temperature. Scaling of the structure factor shows a globular structure of i.corA at a low temperature with an effective dimension D ∼ 3 and a random coil at a high temperature with D ∼ 2. The residue distribution in o.corA is slightly sparser than that of i.corA in a narrow thermos-responsive regime. The difference in thermos-response characteristics of these components (i.corA and o.corA) may reflect their unique transmembrane functions.
Collapse
Affiliation(s)
- Sunan Kitjaruwankul
- Faculty of Science at Sriracha, Kasetsart University Sriracha Campus, Chonburi 20230, Thailand
| | - Channarong Khrutto
- Department of Chemistry, Chulalongkorn University, Bangkok 10330, Thailand
| | | | - B L Farmer
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright Patterson, Air Force Base, Ohio 45433, USA
| | - R B Pandey
- Department of Physics and Astronomy, University of Southern Mississippi, Hattiesburg, Mississippi 39406, USA
| |
Collapse
|
22
|
Matthies D, Dalmas O, Borgnia MJ, Dominik PK, Merk A, Rao P, Reddy BG, Islam S, Bartesaghi A, Perozo E, Subramaniam S. Cryo-EM Structures of the Magnesium Channel CorA Reveal Symmetry Break upon Gating. Cell 2016; 164:747-56. [PMID: 26871634 DOI: 10.1016/j.cell.2015.12.055] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 11/10/2015] [Accepted: 12/23/2015] [Indexed: 11/30/2022]
Abstract
CorA, the major Mg(2+) uptake system in prokaryotes, is gated by intracellular Mg(2+) (KD ∼ 1-2 mM). X-ray crystallographic studies of CorA show similar conformations under Mg(2+)-bound and Mg(2+)-free conditions, but EPR spectroscopic studies reveal large Mg(2+)-driven quaternary conformational changes. Here, we determined cryo-EM structures of CorA in the Mg(2+)-bound closed conformation and in two open Mg(2+)-free states at resolutions of 3.8, 7.1, and 7.1 Å, respectively. In the absence of bound Mg(2+), four of the five subunits are displaced to variable extents (∼ 10-25 Å) by hinge-like motions as large as ∼ 35° at the stalk helix. The transition between a single 5-fold symmetric closed state and an ensemble of low Mg(2+), open, asymmetric conformational states is, thus, the key structural signature of CorA gating. This mechanism is likely to apply to other structurally similar divalent ion channels.
Collapse
Affiliation(s)
- Doreen Matthies
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Olivier Dalmas
- Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
| | - Mario J Borgnia
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Pawel K Dominik
- Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
| | - Alan Merk
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Prashant Rao
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Bharat G Reddy
- Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
| | - Shahidul Islam
- Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
| | - Alberto Bartesaghi
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Eduardo Perozo
- Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA.
| | - Sriram Subramaniam
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
| |
Collapse
|
23
|
Kwolek U, Jamróz D, Janiczek M, Nowakowska M, Wydro P, Kepczynski M. Interactions of Polyethylenimines with Zwitterionic and Anionic Lipid Membranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:5004-5018. [PMID: 27115556 DOI: 10.1021/acs.langmuir.6b00490] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Interactions between polyethylenimines (PEIs) and phospholipid membranes are of fundamental importance for various biophysical applications of these polymers such as gene delivery. Despite investigations into the nature of these interactions, their molecular basis remains poorly understood. In this article, we combined experimental methods and atomistic molecular dynamics (MD) simulations to obtain comprehensive insight into the effect of linear and branched PEIs on zwitterionic and anionic bilayers used as simple models of mammalian cellular membranes. Our results show that PEIs adsorb only partially on the surface of zwitterionic membranes by forming hydrogen bonds to the lipid headgroups, whereas a large part of the polymer chains dangles freely in the aqueous phase. In contrast, PEIs readily adhere to and insert into the anionic membrane. The attraction of the polymer chains to the membrane is due to electrostatic interactions as well as hydrogen bonding between the amine groups of PEI and the phosphate groups of lipids. These interactions were found to induce a substantial reorganization of the bilayer in the polymer vicinity due to the reorientation of lipid molecules. The lipid headgroups were pulled toward the center of the membrane, which can facilitate transmembrane translocations of anionic lipids. Furthermore, the PEI-lipid interactions affect the stability of liposomal dispersions, but we did not see any evidence of disruption of the vesicular structures into small fragments at polymer concentrations typically used in gene therapy. Our results provide a detailed molecular-level description of the lipid organization in the membrane in the presence of polycations that can be useful in understanding their mechanisms of in vitro and in vivo cytotoxicity.
Collapse
Affiliation(s)
- Urszula Kwolek
- Faculty of Chemistry, Jagiellonian University , Ingardena 3, 30-060 Kraków, Poland
| | - Dorota Jamróz
- Faculty of Chemistry, Jagiellonian University , Ingardena 3, 30-060 Kraków, Poland
| | - Małgorzata Janiczek
- Faculty of Chemistry, Jagiellonian University , Ingardena 3, 30-060 Kraków, Poland
| | - Maria Nowakowska
- Faculty of Chemistry, Jagiellonian University , Ingardena 3, 30-060 Kraków, Poland
| | - Paweł Wydro
- Faculty of Chemistry, Jagiellonian University , Ingardena 3, 30-060 Kraków, Poland
| | - Mariusz Kepczynski
- Faculty of Chemistry, Jagiellonian University , Ingardena 3, 30-060 Kraków, Poland
| |
Collapse
|
24
|
Kitjaruwankul S, Wapeesittipan P, Boonamnaj P, Sompornpisut P. Inner and Outer Coordination Shells of Mg(2+) in CorA Selectivity Filter from Molecular Dynamics Simulations. J Phys Chem B 2016; 120:406-17. [PMID: 26727882 DOI: 10.1021/acs.jpcb.5b10925] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Structural data of CorA Mg(2+) channels show that the five Gly-Met-Asn (GMN) motifs at the periplasmic loop of the pentamer structure form a molecular scaffold serving as a selectivity filter. Unfortunately, knowledge about the cation selectivity of Mg(2+) channels remains limited. Since Mg(2+) in aqueous solution has a strong first hydration shell and apparent second hydration sphere, the coordination structure of Mg(2+) in a CorA selectivity filter is expected to be different from that in bulk water. Hence, this study investigated the hydration structure and ligand coordination of Mg(2+) in a selectivity filter of CorA using molecular dynamics (MD) simulations. The simulations reveal that the inner-shell structure of Mg(2+) in the filter is not significantly different from that in aqueous solution. The major difference is the characteristic structural features of the outer shell. The GMN residues engage indirectly in the interactions with the metal ion as ligands in the second shell of Mg(2+). Loss of hydrogen bonds between inner- and outer-shell waters observed from Mg(2+) in bulk water is mostly compensated by interactions between waters in the first solvation shell and the GMN motif. Some water molecules in the second shell remain in the selectivity filter and become less mobile to support the metal binding. Removal of Mg(2+) from the divalent cation sensor sites of the protein had an impact on the structure and metal binding of the filter. From the results, it can be concluded that the GMN motif enhances the affinity of the metal binding site in the CorA selectivity filter by acting as an outer coordination ligand.
Collapse
Affiliation(s)
- Sunan Kitjaruwankul
- Graduate School of Nanoscience and Technology, Chulalongkorn University , Bangkok 10330, Thailand.,Department of Chemistry, Faculty of Science, Chulalongkorn University , Bangkok 10330, Thailand
| | - Pattama Wapeesittipan
- Department of Chemistry, Faculty of Science, Chulalongkorn University , Bangkok 10330, Thailand
| | - Panisak Boonamnaj
- Department of Chemistry, Faculty of Science, Chulalongkorn University , Bangkok 10330, Thailand
| | - Pornthep Sompornpisut
- Department of Chemistry, Faculty of Science, Chulalongkorn University , Bangkok 10330, Thailand
| |
Collapse
|
25
|
Bačová P, Rissanou AN, Harmandaris V. Edge-Functionalized Graphene as a Nanofiller: Molecular Dynamics Simulation Study. Macromolecules 2015. [DOI: 10.1021/acs.macromol.5b01782] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Petra Bačová
- Institute
of Applied and Computational Mathematics (IACM), Foundation for Research and Technology Hellas (FORTH), GR-71110 Heraklion, Crete, Greece
| | - Anastassia N. Rissanou
- Institute
of Applied and Computational Mathematics (IACM), Foundation for Research and Technology Hellas (FORTH), GR-71110 Heraklion, Crete, Greece
| | - Vagelis Harmandaris
- Institute
of Applied and Computational Mathematics (IACM), Foundation for Research and Technology Hellas (FORTH), GR-71110 Heraklion, Crete, Greece
- Department
of Mathematics and Applied Mathematics, University of Crete, GR-71409 Heraklion, Crete, Greece
| |
Collapse
|
26
|
Nishizawa M, Nishizawa K. Free energy of helical transmembrane peptide dimerization in OPLS-AA/Berger force field simulations: inaccuracy and implications for partner-specific Lennard-Jones parameters between peptides and lipids. MOLECULAR SIMULATION 2015. [DOI: 10.1080/08927022.2015.1112006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
27
|
Nishizawa M, Nishizawa K. Potential of mean force analysis of the self-association of leucine-rich transmembrane α-helices: difference between atomistic and coarse-grained simulations. J Chem Phys 2015; 141:075101. [PMID: 25149815 DOI: 10.1063/1.4891932] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Interaction of transmembrane (TM) proteins is important in many biological processes. Large-scale computational studies using coarse-grained (CG) simulations are becoming popular. However, most CG model parameters have not fully been calibrated with respect to lateral interactions of TM peptide segments. Here, we compare the potential of mean forces (PMFs) of dimerization of TM helices obtained using a MARTINI CG model and an atomistic (AT) Berger lipids-OPLS/AA model (AT(OPLS)). For helical, tryptophan-flanked, leucine-rich peptides (WL15 and WALP15) embedded in a parallel configuration in an octane slab, the AT(OPLS) PMF profiles showed a shallow minimum (with a depth of approximately 3 kJ/mol; i.e., a weak tendency to dimerize). A similar analysis using the CHARMM36 all-atom model (AT(CHARMM)) showed comparable results. In contrast, the CG analysis generally showed steep PMF curves with depths of approximately 16-22 kJ/mol, suggesting a stronger tendency to dimerize compared to the AT model. This CG > AT discrepancy in the propensity for dimerization was also seen for dilauroylphosphatidylcholine (DLPC)-embedded peptides. For a WL15 (and WALP15)/DLPC bilayer system, AT(OPLS) PMF showed a repulsive mean force for a wide range of interhelical distances, in contrast to the attractive forces observed in the octane system. The change from the octane slab to the DLPC bilayer also mitigated the dimerization propensity in the CG system. The dimerization energies of CG (AALALAA)3 peptides in DLPC and dioleoylphosphatidylcholine bilayers were in good agreement with previous experimental data. The lipid headgroup, but not the length of the lipid tails, was a key causative factor contributing to the differences between octane and DLPC. Furthermore, the CG model, but not the AT model, showed high sensitivity to changes in amino acid residues located near the lipid-water interface and hydrophobic mismatch between the peptides and membrane. These findings may help interpret CG and AT simulation results on membrane proteins.
Collapse
Affiliation(s)
- Manami Nishizawa
- Teikyo University School of Medical Technology, Itabashi, Tokyo, Japan
| | | |
Collapse
|
28
|
Neale C, Chakrabarti N, Pomorski P, Pai EF, Pomès R. Hydrophobic Gating of Ion Permeation in Magnesium Channel CorA. PLoS Comput Biol 2015; 11:e1004303. [PMID: 26181442 PMCID: PMC4504495 DOI: 10.1371/journal.pcbi.1004303] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 04/28/2015] [Indexed: 12/17/2022] Open
Abstract
Ion channels catalyze ionic permeation across membranes via water-filled pores. To understand how changes in intracellular magnesium concentration regulate the influx of Mg2+ into cells, we examine early events in the relaxation of Mg2+ channel CorA toward its open state using massively-repeated molecular dynamics simulations conducted either with or without regulatory ions. The pore of CorA contains a 2-nm-long hydrophobic bottleneck which remained dehydrated in most simulations. However, rapid hydration or “wetting” events concurrent with small-amplitude fluctuations in pore diameter occurred spontaneously and reversibly. In the absence of regulatory ions, wetting transitions are more likely and include a wet state that is significantly more stable and more hydrated. The free energy profile for Mg2+ permeation presents a barrier whose magnitude is anticorrelated to pore diameter and the extent of hydrophobic hydration. These findings support an allosteric mechanism whereby wetting of a hydrophobic gate couples changes in intracellular magnesium concentration to the onset of ionic conduction. This study shows how rapid wetting/dewetting transitions in the pores of ion channels participate in the control of biological ion permeation. Ion channels catalyze ionic permeation across non-polar membranes via water-filled pores. However, non-polar stretches or hydrophobic bottlenecks are present in the pores of many ion channels. To clarify the relationship between channel regulation, pore hydration, and ion permeation, we examine how the slow relaxation of magnesium channel CorA from its closed state towards its open state modulates wetting of its hydrophobic bottleneck. Results provide a quantitative description of wetting and dewetting probabilities and kinetics and a quantitative relationship between the extent of pore hydration and the energetics of ion permeation, consistent with a mechanism of hydrophobic gating.
Collapse
Affiliation(s)
- Chris Neale
- Molecular Structure and Function, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Nilmadhab Chakrabarti
- Molecular Structure and Function, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Pawel Pomorski
- Shared Hierarchical Academic Research Computing Network, Department of Physics and Astronomy, University of Waterloo, Waterloo, Ontario, Canada
| | - Emil F. Pai
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Ontario Cancer Institute/Princess Margaret Cancer Centre, Campbell Family Institute for Cancer Research, Toronto, Ontario, Canada
| | - Régis Pomès
- Molecular Structure and Function, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
| |
Collapse
|
29
|
Correa-Basurto J, Cuevas-Hernández RI, Phillips-Farfán BV, Martínez-Archundia M, Romo-Mancillas A, Ramírez-Salinas GL, Pérez-González ÓA, Trujillo-Ferrara J, Mendoza-Torreblanca JG. Identification of the antiepileptic racetam binding site in the synaptic vesicle protein 2A by molecular dynamics and docking simulations. Front Cell Neurosci 2015; 9:125. [PMID: 25914622 PMCID: PMC4392693 DOI: 10.3389/fncel.2015.00125] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 03/17/2015] [Indexed: 01/21/2023] Open
Abstract
Synaptic vesicle protein 2A (SV2A) is an integral membrane protein necessary for the proper function of the central nervous system and is associated to the physiopathology of epilepsy. SV2A is the molecular target of the anti-epileptic drug levetiracetam and its racetam analogs. The racetam binding site in SV2A and the non-covalent interactions between racetams and SV2A are currently unknown; therefore, an in silico study was performed to explore these issues. Since SV2A has not been structurally characterized with X-ray crystallography or nuclear magnetic resonance, a three-dimensional (3D) model was built. The model was refined by performing a molecular dynamics simulation (MDS) and the interactions of SV2A with the racetams were determined by docking studies. A reliable 3D model of SV2A was obtained; it reached structural equilibrium during the last 15 ns of the MDS (50 ns) with remaining structural motions in the N-terminus and long cytoplasmic loop. The docking studies revealed that hydrophobic interactions and hydrogen bonds participate importantly in ligand recognition within the binding site. Residues T456, S665, W666, D670 and L689 were important for racetam binding within the trans-membrane hydrophilic core of SV2A. Identifying the racetam binding site within SV2A should facilitate the synthesis of suitable radio-ligands to study treatment response and possibly epilepsy progression.
Collapse
Affiliation(s)
- José Correa-Basurto
- Laboratorio de Modelado Molecular y Diseño de fármacos, Departamento de Bioquímica de la Escuela Superior de Medicina del Instituto Politécnico Nacional, México City Mexico
| | - Roberto I Cuevas-Hernández
- Laboratorio de Modelado Molecular y Diseño de fármacos, Departamento de Bioquímica de la Escuela Superior de Medicina del Instituto Politécnico Nacional, México City Mexico
| | - Bryan V Phillips-Farfán
- Laboratorio de Nutrición Experimental, Laboratorio de Oncología Experimental and Laboratorio de Neuroquímica, Instituto Nacional de Pediatría, México City Mexico
| | - Marlet Martínez-Archundia
- Laboratorio de Modelado Molecular y Diseño de fármacos, Departamento de Bioquímica de la Escuela Superior de Medicina del Instituto Politécnico Nacional, México City Mexico
| | - Antonio Romo-Mancillas
- División de Estudios de Posgrado, Facultad de Química, Universidad Autónoma de Querétaro, Santiago de Querétaro Mexico
| | - Gema L Ramírez-Salinas
- Laboratorio de Modelado Molecular y Diseño de fármacos, Departamento de Bioquímica de la Escuela Superior de Medicina del Instituto Politécnico Nacional, México City Mexico
| | - Óscar A Pérez-González
- Laboratorio de Nutrición Experimental, Laboratorio de Oncología Experimental and Laboratorio de Neuroquímica, Instituto Nacional de Pediatría, México City Mexico
| | - José Trujillo-Ferrara
- Laboratorio de Modelado Molecular y Diseño de fármacos, Departamento de Bioquímica de la Escuela Superior de Medicina del Instituto Politécnico Nacional, México City Mexico
| | - Julieta G Mendoza-Torreblanca
- Laboratorio de Nutrición Experimental, Laboratorio de Oncología Experimental and Laboratorio de Neuroquímica, Instituto Nacional de Pediatría, México City Mexico
| |
Collapse
|
30
|
Faber S, Zinn GM, Boggess A, Fahrenholz T, Kern JC, Kingston HMS. A cleanroom sleeping environment's impact on markers of oxidative stress, immune dysregulation, and behavior in children with autism spectrum disorders. BMC COMPLEMENTARY AND ALTERNATIVE MEDICINE 2015; 15:71. [PMID: 25887094 PMCID: PMC4374395 DOI: 10.1186/s12906-015-0564-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 02/19/2015] [Indexed: 11/24/2022]
Abstract
BACKGROUND An emerging paradigm suggests children with autism display a unique pattern of environmental, genetic, and epigenetic triggers that make them susceptible to developing dysfunctional heavy metal and chemical detoxification systems. These abnormalities could be caused by alterations in the methylation, sulfation, and metalloprotein pathways. This study sought to evaluate the physiological and behavioral effects of children with autism sleeping in an International Organization for Standardization Class 5 cleanroom. METHODS Ten children with autism, ages 3-12, slept in a cleanroom for two weeks to evaluate changes in toxin levels, oxidative stress, immune dysregulation, and behavior. Before and after the children slept in the cleanroom, samples of blood and hair and rating scale scores were obtained to assess these changes. RESULTS Five children significantly lowered their concentration of oxidized glutathione, a biomarker of oxidative stress. The younger cohort, age 5 and under, showed significantly greater mean decreases in two markers of immune dysregulation, CD3% and CD4%, than the older cohort. Changes in serum magnesium, influencing neuronal regulation, correlated negatively while changes in serum iron, affecting oxygenation of tissues, correlated positively with age. Changes in serum benzene and PCB 28 concentrations showed significant negative correlations with age. The younger children demonstrated significant improvements on behavioral rating scales compared to the older children. In a younger pair of identical twins, one twin showed significantly greater improvements in 4 out of 5 markers of oxidative stress, which corresponded with better overall behavioral rating scale scores than the other twin. CONCLUSIONS Younger children who slept in the cleanroom altered elemental levels, decreased immune dysregulation, and improved behavioral rating scales, suggesting that their detoxification metabolism was briefly enhanced. The older children displayed a worsening in behavioral rating scale performance, which may have been caused by the mobilization of toxins from their tissues. The interpretation of this exploratory study is limited by lack of a control group and small sample size. The changes in physiology and behavior noted suggest that performance of larger, prospective controlled studies of exposure to nighttime or 24 hour cleanroom conditions for longer time periods may be useful for understanding detoxification in children with autism. TRIAL REGISTRATION Clinical Trial Registration Number NCT02195401 (Obtained July 18, 2014).
Collapse
Affiliation(s)
- Scott Faber
- Medicine, The Children's Institute, 1405 Shady Avenue, Pittsburgh, PA, 15217, USA.
| | - Gregory M Zinn
- Chemistry and Biochemistry, Duquesne University, 600 Forbes Avenue, Pittsburgh, PA, 15282, USA.
| | - Andrew Boggess
- Chemistry and Biochemistry, Duquesne University, 600 Forbes Avenue, Pittsburgh, PA, 15282, USA.
| | - Timothy Fahrenholz
- Chemistry and Biochemistry, Duquesne University, 600 Forbes Avenue, Pittsburgh, PA, 15282, USA.
| | - John C Kern
- Mathematics and Computer Science, Duquesne University, 600 Forbes Avenue, Pittsburgh, PA, 15282, USA.
| | - H M Skip Kingston
- Chemistry and Biochemistry, Duquesne University, 600 Forbes Avenue, Pittsburgh, PA, 15282, USA.
| |
Collapse
|
31
|
Massink A, Gutiérrez-de-Terán H, Lenselink EB, Ortiz Zacarías NV, Xia L, Heitman LH, Katritch V, Stevens RC, IJzerman AP. Sodium ion binding pocket mutations and adenosine A2A receptor function. Mol Pharmacol 2014; 87:305-13. [PMID: 25473121 DOI: 10.1124/mol.114.095737] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Recently we identified a sodium ion binding pocket in a high-resolution structure of the human adenosine A2A receptor. In the present study we explored this binding site through site-directed mutagenesis and molecular dynamics simulations. Amino acids in the pocket were mutated to alanine, and their influence on agonist and antagonist affinity, allosterism by sodium ions and amilorides, and receptor functionality was explored. Mutation of the polar residues in the Na(+) pocket were shown to either abrogate (D52A(2.50) and N284A(7.49)) or reduce (S91A(3.39), W246A(6.48), and N280A(7.45)) the negative allosteric effect of sodium ions on agonist binding. Mutations D52A(2.50) and N284A(7.49) completely abolished receptor signaling, whereas mutations S91A(3.39) and N280A(7.45) elevated basal activity and mutations S91A(3.39), W246A(6.48), and N280A(7.45) decreased agonist-stimulated receptor signaling. In molecular dynamics simulations D52A(2.50) directly affected the mobility of sodium ions, which readily migrated to another pocket formed by Glu13(1.39) and His278(7.43). The D52A(2.50) mutation also decreased the potency of amiloride with respect to ligand displacement but did not change orthosteric ligand affinity. In contrast, W246A(6.48) increased some of the allosteric effects of sodium ions and amiloride, whereas orthosteric ligand binding was decreased. These new findings suggest that the sodium ion in the allosteric binding pocket not only impacts ligand affinity but also plays a vital role in receptor signaling. Because the sodium ion binding pocket is highly conserved in other class A G protein-coupled receptors, our findings may have a general relevance for these receptors and may guide the design of novel synthetic allosteric modulators or bitopic ligands.
Collapse
Affiliation(s)
- Arnault Massink
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands (A.M., E.B.L., N.V.O.Z., L.X., L.H.H., A.P.IJ.); Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden (H.G.T.); and Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California (V.K., R.C.S.)
| | - Hugo Gutiérrez-de-Terán
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands (A.M., E.B.L., N.V.O.Z., L.X., L.H.H., A.P.IJ.); Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden (H.G.T.); and Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California (V.K., R.C.S.)
| | - Eelke B Lenselink
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands (A.M., E.B.L., N.V.O.Z., L.X., L.H.H., A.P.IJ.); Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden (H.G.T.); and Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California (V.K., R.C.S.)
| | - Natalia V Ortiz Zacarías
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands (A.M., E.B.L., N.V.O.Z., L.X., L.H.H., A.P.IJ.); Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden (H.G.T.); and Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California (V.K., R.C.S.)
| | - Lizi Xia
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands (A.M., E.B.L., N.V.O.Z., L.X., L.H.H., A.P.IJ.); Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden (H.G.T.); and Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California (V.K., R.C.S.)
| | - Laura H Heitman
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands (A.M., E.B.L., N.V.O.Z., L.X., L.H.H., A.P.IJ.); Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden (H.G.T.); and Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California (V.K., R.C.S.)
| | - Vsevolod Katritch
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands (A.M., E.B.L., N.V.O.Z., L.X., L.H.H., A.P.IJ.); Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden (H.G.T.); and Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California (V.K., R.C.S.)
| | - Raymond C Stevens
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands (A.M., E.B.L., N.V.O.Z., L.X., L.H.H., A.P.IJ.); Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden (H.G.T.); and Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California (V.K., R.C.S.)
| | - Adriaan P IJzerman
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands (A.M., E.B.L., N.V.O.Z., L.X., L.H.H., A.P.IJ.); Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden (H.G.T.); and Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California (V.K., R.C.S.)
| |
Collapse
|
32
|
Abstract
The stability of liquids under solvophobic confinement can tip in favor of the vapor phase, nucleating a liquid-to-vapor phase transition that induces attractive forces between confining surfaces. In the case of water adjacent to hydrophobic surfaces, experimental and theoretical evidence support confinement-mediated evaporation stabilization of biomolecular and colloidal assemblies. The macroscopic thermodynamic theory of cavitation under confinement establishes the connection between the size of the confining surfaces, interfacial free energies, and bulk solvent pressure with the critical evaporation separation and interfacial forces. While molecular simulations have confirmed the broad theoretical trends, a quantitative comparison based on independent measurements of the interfacial free energies and liquid-vapor coexistence properties has, to the best of our knowledge, not yet been performed. To overcome the challenges of simulating a large number of systems to validate scaling predictions for a three-dimensional fluid, we simulate both the forces and liquid-vapor coexistence properties of a two-dimensional Lennard-Jones fluid confined between solvophobic plates over a range of plate sizes and reservoir pressures. Our simulations quantitatively agree with theoretical predictions for solvent-mediated forces and critical evaporation separations once the length dependence of the solvation free energy of an individual confining plate is taken into account. The effective solid-liquid line tension length dependence results from molecular scale correlations for solvating microscopic plates and asymptotically decays to the macroscopic value for plates longer than 150 solvent diameters. The success of the macroscopic thermodynamic theory at describing two-dimensional liquids suggests application to surfactant monolayers to experimentally confirm confinement-mediated cavitation.
Collapse
Affiliation(s)
- Henry S Ashbaugh
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, USA.
| |
Collapse
|
33
|
General rules for the arrangements and gating motions of pore-lining helices in homomeric ion channels. Nat Commun 2014; 5:4641. [PMID: 25105557 PMCID: PMC4133698 DOI: 10.1038/ncomms5641] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 07/09/2014] [Indexed: 12/20/2022] Open
Abstract
The pore-lining helix (PLH) bundles are central to the function of all ion channels,
as their conformational rearrangements dictate channel gating. Here we explore all
plausible oligomeric arrangements of the PLH bundles within homomeric ion channels
by building models using generic restraints. In particular, the distance between two
neighbouring PLHs was bounded both below and above in order to avoid steric clash
and allow proper packing. The resulting models provide a theoretical representation
of the accessible space for oligomeric arrangements. While the represented space is
confined, it encompasses nearly all the ion channel PLH bundles for which the
structures are currently known. For a multitude of channels, gating models suggested
by paths within the confined accessible space are in qualitative agreement with
those established in previous structural and computational studies. Rearrangements of the pore-lining helix (PLH) bundles of ion channels
are central to their gating mechanisms. Here, Dai et al. use a modelling approach
to define the general rules that govern the arrangements and gating motions of the PLHs
in homomeric ion channels.
Collapse
|
34
|
Dalmas O, Sompornpisut P, Bezanilla F, Perozo E. Molecular mechanism of Mg2+-dependent gating in CorA. Nat Commun 2014; 5:3590. [PMID: 24694723 PMCID: PMC4066822 DOI: 10.1038/ncomms4590] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 03/07/2014] [Indexed: 11/09/2022] Open
Abstract
CorA is the major transport system responsible for Mg2+ uptake in bacteria and can functionally substitute for its homologue Mrs2p in the yeast inner mitochondrial membrane. Although several CorA crystal structures are available, the molecular mechanism of Mg2+ uptake remains to be established. Here we use EPR spectroscopy, electrophysiology and molecular dynamic simulations to show that CorA is regulated by cytoplasmic Mg2+ acting as a ligand and elucidate the basic conformational rearrangements responsible for Mg2+-dependent gating. Mg2+ unbinding at the divalent cation sensor triggers a conformational change that leads to the inward motion of the stalk helix, which propagates to the pore forming transmembrane helix TM1. Helical tilting and rotation in TM1 generates an iris-like motion that increases the diameter of the permeation pathway, triggering ion conduction. This work establishes the molecular basis of a Mg2+-driven negative feedback loop in CorA as the key physiological event controlling Mg2+ uptake and homeostasis in prokaryotes.
Collapse
Affiliation(s)
- Olivier Dalmas
- Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, 929 E. 57th Street, Chicago, Illinois 60637, USA
| | - Pornthep Sompornpisut
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Francisco Bezanilla
- Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, 929 E. 57th Street, Chicago, Illinois 60637, USA
| | - Eduardo Perozo
- Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, 929 E. 57th Street, Chicago, Illinois 60637, USA
| |
Collapse
|
35
|
Morgan D, Musset B, Kulleperuma K, Smith SME, Rajan S, Cherny VV, Pomès R, DeCoursey TE. Peregrination of the selectivity filter delineates the pore of the human voltage-gated proton channel hHV1. ACTA ACUST UNITED AC 2013; 142:625-40. [PMID: 24218398 PMCID: PMC3840923 DOI: 10.1085/jgp.201311045] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Extraordinary selectivity is crucial to all proton-conducting molecules, including the human voltage-gated proton channel (hHV1), because the proton concentration is >106 times lower than that of other cations. Here we use “selectivity filter scanning” to elucidate the molecular requirements for proton-specific conduction in hHV1. Asp112, in the middle of the S1 transmembrane helix, is an essential part of the selectivity filter in wild-type (WT) channels. After neutralizing Asp112 by mutating it to Ala (D112A), we introduced Asp at each position along S1 from 108 to 118, searching for “second site suppressor” activity. Surprisingly, most mutants lacked even the anion conduction exhibited by D112A. Proton-specific conduction was restored only with Asp or Glu at position 116. The D112V/V116D channel strikingly resembled WT in selectivity, kinetics, and ΔpH-dependent gating. The S4 segment of this mutant has similar accessibility to WT in open channels, because R211H/D112V/V116D was inhibited by internally applied Zn2+. Asp at position 109 allowed anion permeation in combination with D112A but did not rescue function in the nonconducting D112V mutant, indicating that selectivity is established externally to the constriction at F150. The three positions that permitted conduction all line the pore in our homology model, clearly delineating the conduction pathway. Evidently, a carboxyl group must face the pore directly to enable conduction. Molecular dynamics simulations indicate reorganization of hydrogen bond networks in the external vestibule in D112V/V116D. At both positions where it produces proton selectivity, Asp frequently engages in salt linkage with one or more Arg residues from S4. Surprisingly, mean hydration profiles were similar in proton-selective, anion-permeable, and nonconducting constructs. That the selectivity filter functions in a new location helps to define local environmental features required to produce proton-selective conduction.
Collapse
Affiliation(s)
- Deri Morgan
- Department of Molecular Biophysics and Physiology, Rush University, Chicago, IL 60612
| | | | | | | | | | | | | | | |
Collapse
|
36
|
Gutiérrez-de-Terán H, Massink A, Rodríguez D, Liu W, Han GW, Joseph JS, Katritch I, Heitman LH, Xia L, Ijzerman AP, Cherezov V, Katritch V, Stevens RC. The role of a sodium ion binding site in the allosteric modulation of the A(2A) adenosine G protein-coupled receptor. Structure 2013; 21:2175-85. [PMID: 24210756 DOI: 10.1016/j.str.2013.09.020] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 09/25/2013] [Accepted: 09/27/2013] [Indexed: 12/14/2022]
Abstract
The function of G protein-coupled receptors (GPCRs) can be modulated by a number of endogenous allosteric molecules. In this study, we used molecular dynamics, radioligand binding, and thermostability experiments to elucidate the role of the recently discovered sodium ion binding site in the allosteric modulation of the human A(2A) adenosine receptor, conserved among class A GPCRs. While the binding of antagonists and sodium ions to the receptor was noncompetitive in nature, the binding of agonists and sodium ions appears to require mutually exclusive conformational states of the receptor. Amiloride analogs can also bind to the sodium binding pocket, showing distinct patterns of agonist and antagonist modulation. These findings suggest that physiological concentrations of sodium ions affect functionally relevant conformational states of GPCRs and can help to design novel synthetic allosteric modulators or bitopic ligands exploiting the sodium ion binding pocket.
Collapse
Affiliation(s)
- Hugo Gutiérrez-de-Terán
- Fundación Pública Galega de Medicina Xenómica, Hospital Clínico Universitario de Santiago, E-15706 Santiago de Compostela, Spain; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
37
|
Abel S, Lorieau A, de Foresta B, Dupradeau FY, Marchi M. Bindings of hMRP1 transmembrane peptides with dodecylphosphocholine and dodecyl-β-d-maltoside micelles: a molecular dynamics simulation study. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1838:493-509. [PMID: 24157718 DOI: 10.1016/j.bbamem.2013.10.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2013] [Revised: 09/17/2013] [Accepted: 10/14/2013] [Indexed: 12/24/2022]
Abstract
In this paper, we describe molecular dynamics simulation results of the interactions between four peptides (mTM10, mTM16, TM17 and KTM17) with micelles of dodecylphosphocholine (DPC) and dodecyl-β-d-maltoside (DDM). These peptides represent three transmembrane fragments (TM10, 16 and 17) from the MSD1 and MSD2 membrane-spanning domains of an ABC membrane protein (hMRP1), which play roles in the protein functions. The peptide-micelle complex structures, including the tryptophan accessibility and dynamics were compared to circular dichroism and fluorescence studies obtained in water, trifluoroethanol and with micelles. Our work provides additional results not directly accessible by experiments that give further support to the fact that these peptides adopt an interfacial conformation within the micelles. We also show that the peptides are more buried in DDM than in DPC, and consequently, that they have a larger surface exposure to water in DPC than in DDM. As noted previously by simulations and experiments we have also observed formation of cation-π bonds between the phosphocholine DPC headgroup and Trp peptide residue. Concerning the peptide secondary structures (SS), we find that in TFE their initial helical conformations are maintained during the simulation, whereas in water their initial SS are lost after few nanoseconds of simulation. An intermediate situation is observed with micelles, where the peptides remain partially folded and more structured in DDM than in DPC. Finally, our results show no sign of β-strand structure formation as invoked by far-UV CD experiments even when three identical peptides are simulated either in water or with micelles.
Collapse
Affiliation(s)
- Stéphane Abel
- Commissariat à l'Energie Atomique et aux Energies Alternatives, DSV/iBiTEC-S/SB2SM/LBMS & CNRS UMR 8221, Saclay, France.
| | | | | | | | | |
Collapse
|
38
|
Kulleperuma K, Smith SME, Morgan D, Musset B, Holyoake J, Chakrabarti N, Cherny VV, DeCoursey TE, Pomès R. Construction and validation of a homology model of the human voltage-gated proton channel hHV1. ACTA ACUST UNITED AC 2013; 141:445-65. [PMID: 23530137 PMCID: PMC3607825 DOI: 10.1085/jgp.201210856] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The topological similarity of voltage-gated proton channels (HV1s) to the voltage-sensing domain (VSD) of other voltage-gated ion channels raises the central question of whether HV1s have a similar structure. We present the construction and validation of a homology model of the human HV1 (hHV1). Multiple structural alignment was used to construct structural models of the open (proton-conducting) state of hHV1 by exploiting the homology of hHV1 with VSDs of K+ and Na+ channels of known three-dimensional structure. The comparative assessment of structural stability of the homology models and their VSD templates was performed using massively repeated molecular dynamics simulations in which the proteins were allowed to relax from their initial conformation in an explicit membrane mimetic. The analysis of structural deviations from the initial conformation based on up to 125 repeats of 100-ns simulations for each system reveals structural features consistently retained in the homology models and leads to a consensus structural model for hHV1 in which well-defined external and internal salt-bridge networks stabilize the open state. The structural and electrostatic properties of this open-state model are compatible with proton translocation and offer an explanation for the reversal of charge selectivity in neutral mutants of Asp112. Furthermore, these structural properties are consistent with experimental accessibility data, providing a valuable basis for further structural and functional studies of hHV1. Each Arg residue in the S4 helix of hHV1 was replaced by His to test accessibility using Zn2+ as a probe. The two outermost Arg residues in S4 were accessible to external solution, whereas the innermost one was accessible only to the internal solution. Both modeling and experimental data indicate that in the open state, Arg211, the third Arg residue in the S4 helix in hHV1, remains accessible to the internal solution and is located near the charge transfer center, Phe150.
Collapse
Affiliation(s)
- Kethika Kulleperuma
- Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
| | | | | | | | | | | | | | | | | |
Collapse
|
39
|
Schmitz J, Tierbach A, Lenz H, Meschenmoser K, Knoop V. Membrane protein interactions between different Arabidopsis thaliana MRS2-type magnesium transporters are highly permissive. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2032-40. [DOI: 10.1016/j.bbamem.2013.05.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Revised: 05/06/2013] [Accepted: 05/22/2013] [Indexed: 12/25/2022]
|
40
|
Khan MB, Sponder G, Sjöblom B, Svidová S, Schweyen RJ, Carugo O, Djinović-Carugo K. Structural and functional characterization of the N-terminal domain of the yeast Mg2+channel Mrs2. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:1653-64. [DOI: 10.1107/s0907444913011712] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2013] [Accepted: 04/29/2013] [Indexed: 01/08/2023]
|
41
|
Payandeh J, Pfoh R, Pai EF. The structure and regulation of magnesium selective ion channels. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2778-92. [PMID: 23954807 DOI: 10.1016/j.bbamem.2013.08.002] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 07/30/2013] [Accepted: 08/02/2013] [Indexed: 10/26/2022]
Abstract
The magnesium ion (Mg(2+)) is the most abundant divalent cation within cells. In man, Mg(2+)-deficiency is associated with diseases affecting the heart, muscle, bone, immune, and nervous systems. Despite its impact on human health, little is known about the molecular mechanisms that regulate magnesium transport and storage. Complete structural information on eukaryotic Mg(2+)-transport proteins is currently lacking due to associated technical challenges. The prokaryotic MgtE and CorA magnesium transport systems have recently succumbed to structure determination by X-ray crystallography, providing first views of these ubiquitous and essential Mg(2+)-channels. MgtE and CorA are unique among known membrane protein structures, each revealing a novel protein fold containing distinct arrangements of ten transmembrane-spanning α-helices. Structural and functional analyses have established that Mg(2+)-selectivity in MgtE and CorA occurs through distinct mechanisms. Conserved acidic side-chains appear to form the selectivity filter in MgtE, whereas conserved asparagines coordinate hydrated Mg(2+)-ions within the selectivity filter of CorA. Common structural themes have also emerged whereby MgtE and CorA sense and respond to physiologically relevant, intracellular Mg(2+)-levels through dedicated regulatory domains. Within these domains, multiple primary and secondary Mg(2+)-binding sites serve to staple these ion channels into their respective closed conformations, implying that Mg(2+)-transport is well guarded and very tightly regulated. The MgtE and CorA proteins represent valuable structural templates to better understand the related eukaryotic SLC41 and Mrs2-Alr1 magnesium channels. Herein, we review the structure, function and regulation of MgtE and CorA and consider these unique proteins within the expanding universe of ion channel and transporter structural biology.
Collapse
Affiliation(s)
- Jian Payandeh
- Department of Structural Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
| | | | | |
Collapse
|
42
|
Vamparys L, Gautier R, Vanni S, Bennett WFD, Tieleman DP, Antonny B, Etchebest C, Fuchs PFJ. Conical lipids in flat bilayers induce packing defects similar to that induced by positive curvature. Biophys J 2013; 104:585-93. [PMID: 23442909 DOI: 10.1016/j.bpj.2012.11.3836] [Citation(s) in RCA: 116] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 10/15/2012] [Accepted: 11/16/2012] [Indexed: 01/05/2023] Open
Abstract
In biological membranes, changes in lipid composition or mechanical deformations produce defects in the geometrical arrangement of lipids, thus allowing the adsorption of certain peripheral proteins. Here, we perform molecular dynamics simulations on bilayers containing a cylindrical lipid (PC) and a conical lipid (DOG). Profiles of atomic density and lateral pressure across the bilayer show differences in the acyl chain region due to deeper partitioning of DOG compared to PC. However, such analyses are less informative for the interfacial region where peripheral proteins adsorb. To circumvent this limitation, we develop, to our knowledge, a new method of membrane surface analysis. This method allows the identification of chemical defects, where hydrocarbon chains are accessible to the solvent, and geometrical defects, i.e., voids deeper than the glycerol backbone. The size and number of both types of defects increase with the number of monounsaturated acyl chains in PC and with the introduction of DOG, although the defects do not colocalize with the conical lipid. Interestingly, the size and probability of the defects promoted by DOG resemble those induced by positive curvature, thus explaining why conical lipids and positive curvature can both drive the adsorption of peripheral proteins that use hydrophobic residues as membrane anchors.
Collapse
|
43
|
Vanni S, Vamparys L, Gautier R, Drin G, Etchebest C, Fuchs PFJ, Antonny B. Amphipathic lipid packing sensor motifs: probing bilayer defects with hydrophobic residues. Biophys J 2013; 104:575-84. [PMID: 23442908 DOI: 10.1016/j.bpj.2012.11.3837] [Citation(s) in RCA: 132] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Revised: 10/15/2012] [Accepted: 11/16/2012] [Indexed: 11/18/2022] Open
Abstract
Sensing membrane curvature allows fine-tuning of complex reactions that occur at the surface of membrane-bound organelles. One of the most sensitive membrane curvature sensors, the Amphipathic Lipid Packing Sensor (ALPS) motif, does not seem to recognize the curved surface geometry of membranes per se; rather, it recognizes defects in lipid packing that arise from membrane bending. In a companion paper, we show that these defects can be mimicked by introducing conical lipids in a flat lipid bilayer, in agreement with experimental observations. Here, we use molecular-dynamics (MD) simulations to characterize ALPS binding to such lipid bilayers. The ALPS motif recognizes lipid-packing defects by a conserved mechanism: peptide partitioning is driven by the insertion of hydrophobic residues into large packing defects that are preformed in the bilayer. This insertion induces only minor modifications in the statistical distribution of the free packing defects. ALPS insertion is severely hampered when monounsaturated lipids are replaced by saturated lipids, leading to a decrease in packing defects. We propose that the hypersensitivity of ALPS motifs to lipid packing defects results from the repetitive use of hydrophobic insertions along the monotonous ALPS sequence.
Collapse
Affiliation(s)
- Stefano Vanni
- Institut de Pharmacologie Moléculaire et Cellulaire, Université de Nice Sophia-Antipolis and Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7275, Valbonne, France
| | | | | | | | | | | | | |
Collapse
|
44
|
Neale C, Madill C, Rauscher S, Pomès R. Accelerating Convergence in Molecular Dynamics Simulations of Solutes in Lipid Membranes by Conducting a Random Walk along the Bilayer Normal. J Chem Theory Comput 2013; 9:3686-703. [DOI: 10.1021/ct301005b] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Chris Neale
- Molecular Structure
and Function,
The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario,
M5G 1X8, Canada
- Department
of Biochemistry,
University of Toronto, 101 College Street, Toronto, Ontario, M5G 1L7,
Canada
| | - Chris Madill
- Molecular Structure
and Function,
The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario,
M5G 1X8, Canada
- Department
of Biochemistry,
University of Toronto, 101 College Street, Toronto, Ontario, M5G 1L7,
Canada
| | - Sarah Rauscher
- Molecular Structure
and Function,
The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario,
M5G 1X8, Canada
- Department
of Biochemistry,
University of Toronto, 101 College Street, Toronto, Ontario, M5G 1L7,
Canada
| | - Régis Pomès
- Molecular Structure
and Function,
The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario,
M5G 1X8, Canada
- Department
of Biochemistry,
University of Toronto, 101 College Street, Toronto, Ontario, M5G 1L7,
Canada
| |
Collapse
|
45
|
Lenz H, Dombinov V, Dreistein J, Reinhard MR, Gebert M, Knoop V. Magnesium deficiency phenotypes upon multiple knockout of Arabidopsis thaliana MRS2 clade B genes can be ameliorated by concomitantly reduced calcium supply. PLANT & CELL PHYSIOLOGY 2013; 54:1118-31. [PMID: 23628997 DOI: 10.1093/pcp/pct062] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Plant MRS2 membrane protein family members have been shown to play important roles in magnesium uptake and homeostasis. Single and double knockouts for two Arabidopsis thaliana genes, AtMRS2-1 and AtMRS2-5, have previously not shown significant phenotypes even under limiting Mg(2+) supply although both are strongly expressed already in early seedlings. Together with AtMRS2-10, these genes form clade B of the AtMRS2 gene family. We now succeeded in obtaining homozygous AtMRS2-1/10 double and AtMRS2-1/5/10 triple knockout lines after selection under increased magnesium supply. Although wilting early, both new mutant lines develop fully and are also fertile under standard magnesium supply, but show severe developmental retardation under limiting Mg(2+) concentrations. To investigate nutrient dependency of germination and seedling development under various conditions, including variable supplies of Mg(2+), Ca(2+), Zn(2+), Mn(2+), Co(2+), Cd(2+) and Cu(2+), in a reproducible and economical way, we employed a small-scale liquid culturing system in 24-well plate set-ups. This allowed the growth and monitoring of individual plantlets of different mutant lines under several nutritional conditions in parallel, and the scoring and statistical evaluation of developmental stages and biomass accumulation. Detrimental effects of higher concentrations of these elements were similar in mutants and the wild type. However, growth retardation phenotypes seen upon hydroponic cultivation under low Mg(2+) could be ameliorated when Ca(2+) concentrations were concomitantly lowered, supporting indications for an important interplay of these two most abundant divalent cations in the nutrient homeostasis of plants.
Collapse
Affiliation(s)
- Henning Lenz
- Abteilung Molekulare Evolution, IZMB-Institut für Zelluläre und Molekulare Botanik, Universität Bonn, Kirschallee 1, D-53115 Bonn, Germany
| | | | | | | | | | | |
Collapse
|
46
|
Catalysis of Na+ permeation in the bacterial sodium channel Na(V)Ab. Proc Natl Acad Sci U S A 2013; 110:11331-6. [PMID: 23803856 DOI: 10.1073/pnas.1309452110] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Determination of a high-resolution 3D structure of voltage-gated sodium channel Na(V)Ab opens the way to elucidating the mechanism of ion conductance and selectivity. To examine permeation of Na(+) through the selectivity filter of the channel, we performed large-scale molecular dynamics simulations of Na(V)Ab in an explicit, hydrated lipid bilayer at 0 mV in 150 mM NaCl, for a total simulation time of 21.6 μs. Although the cytoplasmic end of the pore is closed, reversible influx and efflux of Na(+) through the selectivity filter occurred spontaneously during simulations, leading to equilibrium movement of Na(+) between the extracellular medium and the central cavity of the channel. Analysis of Na(+) dynamics reveals a knock-on mechanism of ion permeation characterized by alternating occupancy of the channel by 2 and 3 Na(+) ions, with a computed rate of translocation of (6 ± 1) × 10(6) ions⋅s(-1) that is consistent with expectations from electrophysiological studies. The binding of Na(+) is intimately coupled to conformational isomerization of the four E177 side chains lining the extracellular end of the selectivity filter. The reciprocal coordination of variable numbers of Na(+) ions and carboxylate groups leads to their condensation into ionic clusters of variable charge and spatial arrangement. Structural fluctuations of these ionic clusters result in a myriad of ion binding modes and foster a highly degenerate, liquid-like energy landscape propitious to Na(+) diffusion. By stabilizing multiple ionic occupancy states while helping Na(+) ions diffuse within the selectivity filter, the conformational flexibility of E177 side chains underpins the knock-on mechanism of Na(+) permeation.
Collapse
|
47
|
Exploring the structure and function of Thermotoga maritima CorA reveals the mechanism of gating and ion selectivity in Co2+/Mg2+ transport. Biochem J 2013; 451:365-74. [PMID: 23425532 PMCID: PMC3629940 DOI: 10.1042/bj20121745] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The CorA family of divalent cation transporters utilizes Mg2+ and Co2+ as
primary substrates. The molecular mechanism of its function, including ion selectivity and gating,
has not been fully characterized. Recently we reported a new structure of a CorA homologue from
Methanocaldococcus jannaschii, which provided novel structural details that offered
the conception of a unique gating mechanism involving conversion of an open hydrophilic gate into a
closed hydrophobic one. In the present study we report functional evidence for this novel gating
mechanism in the Thermotoga maritima CorA together with an improved crystal
structure of this CorA to 2.7 Å (1 Å=0.1 nm) resolution. The latter reveals the
organization of the selectivity filter to be similar to that of M. jannaschii CorA
and also the previously unknown organization of the second signature motif of the CorA family. The
proposed gating is achieved by a helical rotation upon the binding of a metal ion substrate to the
regulatory binding sites. Additionally, our data suggest that the preference of this CorA for
Co2+ over Mg2+ is controlled by the presence of threonine side chains in the
channel. Finally, the roles of the intracellular metal-binding sites have been assigned to increased
thermostability and regulation of the gating. These mechanisms most likely apply to the entire CorA
family as they are regulated by the highly conserved amino acids.
Collapse
|
48
|
Kapla J, Wohlert J, Stevensson B, Engström O, Widmalm G, Maliniak A. Molecular dynamics simulations of membrane-sugar interactions. J Phys Chem B 2013; 117:6667-73. [PMID: 23662588 DOI: 10.1021/jp402385d] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
It is well documented that disaccharides in general and trehalose (TRH) in particular strongly affect physical properties and functionality of lipid bilayers. We investigate interactions between lipid membranes formed by 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and TRH by means of molecular dynamics (MD) computer simulations. Ten different TRH concentrations were studied in the range wTRH = 0-0.20 (w/w). The potential of mean force (PMF) for DMPC bilayer-TRH interactions was determined using two different force fields, and was subsequently used in a simple analytical model for description of sugar binding at the membrane interface. The MD results were in good agreement with the predictions of the model. The net affinities of TRH for the DMPC bilayer derived from the model and MD simulations were compared with experimental results. The area per lipid increases and the membrane becomes thinner with increased TRH concentration, which is interpreted as an intercalation effect of the TRH molecules into the polar part of the lipids, resulting in conformational changes in the chains. These results are consistent with recent experimental observations. The compressibility modulus related to the fluctuations of the membrane increases dramatically with increased TRH concentration, which indicates higher order and rigidity of the bilayer. This is also reflected in a decrease (by a factor of 15) of the lateral diffusion of the lipids. We interpret these observations as a formation of a glassy state at the interface of the membrane, which has been suggested in the literature as a hypothesis for the membrane-sugar interactions.
Collapse
Affiliation(s)
- Jon Kapla
- Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | | | | | | | | | | |
Collapse
|
49
|
Gu RX, Liu LA, Wang YH, Xu Q, Wei DQ. Structural Comparison of the Wild-Type and Drug-Resistant Mutants of the Influenza A M2 Proton Channel by Molecular Dynamics Simulations. J Phys Chem B 2013; 117:6042-51. [DOI: 10.1021/jp312396q] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Ruo-Xu Gu
- State Key Laboratory of Microbial
Metabolism and Shanghai Jiao Tong University, Shanghai Minhang District,
200240, China
| | - Limin Angela Liu
- Fred Hutchinson
Cancer Research
Center, Seattle Washington 98109, United States
| | - Yong-Hua Wang
- College of Light Industry and
Food Sciences, South China University of Technology, Guangzhou, 510640,
China
| | - Qin Xu
- State Key Laboratory of Microbial
Metabolism and Shanghai Jiao Tong University, Shanghai Minhang District,
200240, China
| | - Dong-Qing Wei
- State Key Laboratory of Microbial
Metabolism and Shanghai Jiao Tong University, Shanghai Minhang District,
200240, China
| |
Collapse
|
50
|
Neale C, Ghanei H, Holyoake J, Bishop RE, Privé GG, Pomès R. Detergent-mediated protein aggregation. Chem Phys Lipids 2013; 169:72-84. [PMID: 23466535 PMCID: PMC5007131 DOI: 10.1016/j.chemphyslip.2013.02.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Revised: 02/14/2013] [Accepted: 02/18/2013] [Indexed: 10/27/2022]
Abstract
Because detergents are commonly used to solvate membrane proteins for structural evaluation, much attention has been devoted to assessing the conformational bias imparted by detergent micelles in comparison to the native environment of the lipid bilayer. Here, we conduct six 500-ns simulations of a system with >600,000 atoms to investigate the spontaneous self assembly of dodecylphosphocholine detergent around multiple molecules of the integral membrane protein PagP. This detergent formed equatorial micelles in which acyl chains surround the protein's hydrophobic belt, confirming existing models of the detergent solvation of membrane proteins. In addition, unexpectedly, the extracellular and periplasmic apical surfaces of PagP interacted with the headgroups of detergents in other micelles 85 and 60% of the time, respectively, forming complexes that were stable for hundreds of nanoseconds. In some cases, an apical surface of one molecule of PagP interacted with an equatorial micelle surrounding another molecule of PagP. In other cases, the apical surfaces of two molecules of PagP simultaneously bound a neat detergent micelle. In these ways, detergents mediated the non-specific aggregation of folded PagP. These simulation results are consistent with dynamic light scattering experiments, which show that, at detergent concentrations ≥600 mM, PagP induces the formation of large scattering species that are likely to contain many copies of the PagP protein. Together, these simulation and experimental results point to a potentially generic mechanism of detergent-mediated protein aggregation.
Collapse
Affiliation(s)
- Chris Neale
- Molecular Structure and Function, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada
- Department of Biochemistry, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Hamed Ghanei
- Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - John Holyoake
- Molecular Structure and Function, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada
- Ontario Cancer Institute and Campbell Family Cancer Research Institute, UHN, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Russell E. Bishop
- Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Gilbert G. Privé
- Department of Biochemistry, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
- Ontario Cancer Institute and Campbell Family Cancer Research Institute, UHN, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Régis Pomès
- Molecular Structure and Function, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada
- Department of Biochemistry, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| |
Collapse
|