1
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Cao Y, Yang R, Wang W, Jiang S, Yang C, Wang Q, Liu N, Xue Y, Lee I, Meng X, Yuan Z. Effects of membrane lipids on phospholamban pentameric channel structure and ion transportation mechanisms. Int J Biol Macromol 2022; 224:766-775. [DOI: 10.1016/j.ijbiomac.2022.10.164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 10/10/2022] [Accepted: 10/19/2022] [Indexed: 11/05/2022]
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2
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Koch D, Alexandrovich A, Funk F, Kho AL, Schmitt JP, Gautel M. Molecular noise filtering in the β-adrenergic signaling network by phospholamban pentamers. Cell Rep 2021; 36:109448. [PMID: 34320358 PMCID: PMC8333238 DOI: 10.1016/j.celrep.2021.109448] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 04/16/2021] [Accepted: 07/05/2021] [Indexed: 02/07/2023] Open
Abstract
Phospholamban (PLN) is an important regulator of cardiac calcium handling due to its ability to inhibit the calcium ATPase SERCA. β-Adrenergic stimulation reverses SERCA inhibition via PLN phosphorylation and facilitates fast calcium reuptake. PLN also forms pentamers whose physiological significance has remained elusive. Using mathematical modeling combined with biochemical and cell biological experiments, we show that pentamers regulate both the dynamics and steady-state levels of monomer phosphorylation. Substrate competition by pentamers and a feed-forward loop involving inhibitor-1 can delay monomer phosphorylation by protein kinase A (PKA), whereas cooperative pentamer dephosphorylation enables bistable PLN steady-state phosphorylation. Simulations show that phosphorylation delay and bistability act as complementary filters that reduce the effect of random fluctuations in PKA activity, thereby ensuring consistent monomer phosphorylation and SERCA activity despite noisy upstream signals. Preliminary analyses suggest that the PLN mutation R14del could impair noise filtering, offering a new perspective on how this mutation causes cardiac arrhythmias.
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Affiliation(s)
- Daniel Koch
- Randall Centre for Cell and Molecular Biophysics, King's College London, SE1 1UL London, UK.
| | | | - Florian Funk
- Institute of Pharmacology and Clinical Pharmacology, and Cardiovascular Research Institute Düsseldorf (CARID), University Hospital Düsseldorf, 40225 Düsseldorf, Germany
| | - Ay Lin Kho
- Randall Centre for Cell and Molecular Biophysics, King's College London, SE1 1UL London, UK
| | - Joachim P Schmitt
- Institute of Pharmacology and Clinical Pharmacology, and Cardiovascular Research Institute Düsseldorf (CARID), University Hospital Düsseldorf, 40225 Düsseldorf, Germany
| | - Mathias Gautel
- Randall Centre for Cell and Molecular Biophysics, King's College London, SE1 1UL London, UK
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3
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Chipot C, Dehez F, Schnell JR, Zitzmann N, Pebay-Peyroula E, Catoire LJ, Miroux B, Kunji ERS, Veglia G, Cross TA, Schanda P. Perturbations of Native Membrane Protein Structure in Alkyl Phosphocholine Detergents: A Critical Assessment of NMR and Biophysical Studies. Chem Rev 2018; 118:3559-3607. [PMID: 29488756 PMCID: PMC5896743 DOI: 10.1021/acs.chemrev.7b00570] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Indexed: 12/25/2022]
Abstract
Membrane proteins perform a host of vital cellular functions. Deciphering the molecular mechanisms whereby they fulfill these functions requires detailed biophysical and structural investigations. Detergents have proven pivotal to extract the protein from its native surroundings. Yet, they provide a milieu that departs significantly from that of the biological membrane, to the extent that the structure, the dynamics, and the interactions of membrane proteins in detergents may considerably vary, as compared to the native environment. Understanding the impact of detergents on membrane proteins is, therefore, crucial to assess the biological relevance of results obtained in detergents. Here, we review the strengths and weaknesses of alkyl phosphocholines (or foscholines), the most widely used detergent in solution-NMR studies of membrane proteins. While this class of detergents is often successful for membrane protein solubilization, a growing list of examples points to destabilizing and denaturing properties, in particular for α-helical membrane proteins. Our comprehensive analysis stresses the importance of stringent controls when working with this class of detergents and when analyzing the structure and dynamics of membrane proteins in alkyl phosphocholine detergents.
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Affiliation(s)
- Christophe Chipot
- SRSMC, UMR 7019 Université de Lorraine CNRS, Vandoeuvre-les-Nancy F-54500, France
- Laboratoire
International Associé CNRS and University of Illinois at Urbana−Champaign, Vandoeuvre-les-Nancy F-54506, France
- Department
of Physics, University of Illinois at Urbana−Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States
| | - François Dehez
- SRSMC, UMR 7019 Université de Lorraine CNRS, Vandoeuvre-les-Nancy F-54500, France
- Laboratoire
International Associé CNRS and University of Illinois at Urbana−Champaign, Vandoeuvre-les-Nancy F-54506, France
| | - Jason R. Schnell
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Nicole Zitzmann
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | | | - Laurent J. Catoire
- Laboratory
of Biology and Physico-Chemistry of Membrane Proteins, Institut de Biologie Physico-Chimique (IBPC), UMR
7099 CNRS, Paris 75005, France
- University
Paris Diderot, Paris 75005, France
- PSL
Research University, Paris 75005, France
| | - Bruno Miroux
- Laboratory
of Biology and Physico-Chemistry of Membrane Proteins, Institut de Biologie Physico-Chimique (IBPC), UMR
7099 CNRS, Paris 75005, France
- University
Paris Diderot, Paris 75005, France
- PSL
Research University, Paris 75005, France
| | - Edmund R. S. Kunji
- Medical
Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Gianluigi Veglia
- Department
of Biochemistry, Molecular Biology, and Biophysics, and Department
of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Timothy A. Cross
- National
High Magnetic Field Laboratory, Florida
State University, Tallahassee, Florida 32310, United States
| | - Paul Schanda
- Université
Grenoble Alpes, CEA, CNRS, IBS, Grenoble F-38000, France
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4
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Smeazzetto S, Tadini-Buoninsegni F, Thiel G, Moncelli MR. Selectivity of the phospholamban ion channel investigated by single channel measurements. J Electroanal Chem (Lausanne) 2018. [DOI: 10.1016/j.jelechem.2018.01.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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5
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Dehez F, Schanda P, King MS, Kunji ERS, Chipot C. Mitochondrial ADP/ATP Carrier in Dodecylphosphocholine Binds Cardiolipins with Non-native Affinity. Biophys J 2017; 113:2311-2315. [PMID: 29056231 PMCID: PMC5722206 DOI: 10.1016/j.bpj.2017.09.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 09/12/2017] [Accepted: 09/21/2017] [Indexed: 12/11/2022] Open
Abstract
Biophysical investigation of membrane proteins generally requires their extraction from native sources using detergents, a step that can lead, possibly irreversibly, to protein denaturation. The propensity of dodecylphosphocholine (DPC), a detergent widely utilized in NMR studies of membrane proteins, to distort their structure has been the subject of much controversy. It has been recently proposed that the binding specificity of the yeast mitochondrial ADP/ATP carrier (yAAC3) toward cardiolipins is preserved in DPC, thereby suggesting that DPC is a suitable environment in which to study membrane proteins. In this communication, we used all-atom molecular dynamics simulations to investigate the specific binding of cardiolipins to yAAC3. Our data demonstrate that the interaction interface observed in a native-like environment differs markedly from that inferred from an NMR investigation in DPC, implying that in this detergent, the protein structure is distorted. We further investigated yAAC3 solubilized in DPC and in the milder dodecylmaltoside with thermal-shift assays. The loss of thermal transition observed in DPC confirms that the protein is no longer properly folded in this environment.
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Affiliation(s)
- François Dehez
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Unité Mixte de Recherche no. 7565, Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - Paul Schanda
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, Grenoble, France.
| | - Martin S King
- Medical Research Council, Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Edmund R S Kunji
- Medical Research Council, Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Christophe Chipot
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Unité Mixte de Recherche no. 7565, Université de Lorraine, Vandœuvre-lès-Nancy, France; Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois.
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6
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Cao Y, Wu X, Wang X, Sun H, Lee I. Transmembrane dynamics of the Thr-5 phosphorylated sarcolipin pentameric channel. Arch Biochem Biophys 2016; 604:143-51. [PMID: 27378083 DOI: 10.1016/j.abb.2016.06.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Revised: 06/23/2016] [Accepted: 06/24/2016] [Indexed: 12/16/2022]
Abstract
Sarcolipin (SLN), an important membrane protein expressed in the sarcoplasmic reticulum (SR), regulates muscle contractions in cardiac and skeletal muscle. The phosphorylation at amino acid Thr5 of the SLN protein modulates the amount of Ca(2+) that passes through the SR. Using molecular dynamics simulation, we evaluated the phosphorylation at Thr5 of pentameric SLN (phospho-SLN) channel's energy barrier and pore characteristics by calculating the potential of mean force (PMF) along the channel pore and determining the diffusion coefficient. The results indicate that pentameric phospho-SLN promotes penetration of monovalent and divalent ions through the channel. The analysis of PMF, pore radius and diffusion coefficient indicates that Leu21 is the hydrophobic gate of the pentameric SLN channel. In the channel, water molecules near the Leu21 pore demonstrated a clear hydrated-dehydrated transition; however, the mutation of Leu21 to an Alanine (L21A) destroyed the hydrated-dehydrated transitions. These water-dynamic behaviors and PMF confirm that Leu21 is the key residue that regulates the ion permeability of the pentameric SLN channel. These results provide the structural-basis insights and molecular-dynamic information that are needed to understand the regulatory mechanisms of ion permeability in the pentameric SLN channel.
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Affiliation(s)
- Yipeng Cao
- Institute of Physics, Nankai University, No.94 Weijin Road, Tianjin, 300071, PR China
| | - Xue Wu
- Institute of Physics, Nankai University, No.94 Weijin Road, Tianjin, 300071, PR China
| | - Xinyu Wang
- Institute of Physics, Nankai University, No.94 Weijin Road, Tianjin, 300071, PR China
| | - Haiying Sun
- Institute of Physics, Nankai University, No.94 Weijin Road, Tianjin, 300071, PR China
| | - Imshik Lee
- Institute of Physics, Nankai University, No.94 Weijin Road, Tianjin, 300071, PR China.
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7
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Guardiani C, Leggio L, Scorciapino MA, de Pinto V, Ceccarelli M. A computational study of ion current modulation in hVDAC3 induced by disulfide bonds. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:813-23. [PMID: 26806159 DOI: 10.1016/j.bbamem.2016.01.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 12/05/2015] [Accepted: 01/19/2016] [Indexed: 11/29/2022]
Abstract
The human VDAC channel exists in three isoforms characterized by high sequence homology and structural similarity. Yet the function and mode of action of hVDAC3 are still elusive. The presence of six surface cysteines exposed to the oxidizing environment of the mitochondrial inter-membrane space suggests the possible establishment of intramolecular disulfide bonds. Two natural candidates for disulfide bridge formation are Cys2 and Cys8 that, located on the flexible N-terminal domain, can easily come in contact. A third potentially important residue is Cys122 that is close to Cys2 in the homology model of VDAC3. Here we analyzed the impact of SS bonds through molecular dynamics simulations of derivatives of hVDAC3 (dubbed SS-2-8, SS-2-122, SS-8-122) including a single disulfide bond. Simulations showed that in SS-8-122, the fragment 1-7 crosses the top part of the barrel partially occluding the pore and causing a 20% drop of conductance. In order to identify other potential channel-occluding disulfide bonds, we used a set of neural networks and structural bioinformatics algorithms, after filtering with the steric constraints imposed by the 3D-structure. We identified other three species, namely SS-8-65, SS-2-36 and SS-8-36. While the conductance of SS-8-65 and SS-2-36 is about 30% lower than that of the species without disulfide bonds, the conductance of SS-8-36 was 40-50% lower. The results show how VDAC3 is able to modulate its pore size and current by exploiting the mobility of the N-terminal and forming, upon external stimuli, disulfide bridges with cysteine residues located on the barrel and exposed to the inter-membrane space.
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Affiliation(s)
- Carlo Guardiani
- Istituto Officina dei Materiali, Consiglio Nazionale delle Ricerche (CNR-IOM), UOS, Cagliari, Italy
| | - Loredana Leggio
- Department of Biomedical and Biotechnological Sciences, BIOMETEC, University of Catania, Italy; National Institute for Biomembranes and Biosystems, Section of Catania, viale A. Doria 6, 95125 Catania, Italy
| | - Mariano Andrea Scorciapino
- Istituto Officina dei Materiali, Consiglio Nazionale delle Ricerche (CNR-IOM), UOS, Cagliari, Italy; Department of Biomedical Sciences, Biochemistry Unit, University of Cagliari, Italy
| | - Vito de Pinto
- Department of Biomedical and Biotechnological Sciences, BIOMETEC, University of Catania, Italy; National Institute for Biomembranes and Biosystems, Section of Catania, viale A. Doria 6, 95125 Catania, Italy
| | - Matteo Ceccarelli
- Istituto Officina dei Materiali, Consiglio Nazionale delle Ricerche (CNR-IOM), UOS, Cagliari, Italy; Department of Physics, University of Cagliari, Cagliari, Italy.
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8
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Pothula KR, Solano CJF, Kleinekathöfer U. Simulations of outer membrane channels and their permeability. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1858:1760-71. [PMID: 26721326 DOI: 10.1016/j.bbamem.2015.12.020] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 12/15/2015] [Accepted: 12/17/2015] [Indexed: 12/25/2022]
Abstract
Channels in the outer membrane of Gram-negative bacteria provide essential pathways for the controlled and unidirectional transport of ions, nutrients and metabolites into the cell. At the same time the outer membrane serves as a physical barrier for the penetration of noxious substances such as antibiotics into the bacteria. Most antibiotics have to pass through these membrane channels to either reach cytoplasmic bound targets or to further cross the hydrophobic inner membrane. Considering the pharmaceutical significance of antibiotics, understanding the functional role and mechanism of these channels is of fundamental importance in developing strategies to design new drugs with enhanced permeation abilities. Due to the biological complexity of membrane channels and experimental limitations, computer simulations have proven to be a powerful tool to investigate the structure, dynamics and interactions of membrane channels. Considerable progress has been made in computer simulations of membrane channels during the last decade. The goal of this review is to provide an overview of the computational techniques and their roles in modeling the transport across outer membrane channels. A special emphasis is put on all-atom molecular dynamics simulations employed to better understand the transport of molecules. Moreover, recent molecular simulations of ion, substrate and antibiotics translocation through membrane pores are briefly summarized. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.
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Affiliation(s)
- Karunakar R Pothula
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Carlos J F Solano
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
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9
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Becucci L, Foresti ML, Schwan A, Guidelli R. Can proton pumping by SERCA enhance the regulatory role of phospholamban and sarcolipin? BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2682-90. [DOI: 10.1016/j.bbamem.2013.07.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Revised: 06/22/2013] [Accepted: 07/08/2013] [Indexed: 11/26/2022]
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10
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Smeazzetto S, Saponaro A, Young HS, Moncelli MR, Thiel G. Structure-function relation of phospholamban: modulation of channel activity as a potential regulator of SERCA activity. PLoS One 2013; 8:e52744. [PMID: 23308118 PMCID: PMC3537670 DOI: 10.1371/journal.pone.0052744] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Accepted: 11/20/2012] [Indexed: 11/22/2022] Open
Abstract
Phospholamban (PLN) is a small integral membrane protein, which binds and inhibits in a yet unknown fashion the Ca2+-ATPase (SERCA) in the sarcoplasmic reticulum. When reconstituted in planar lipid bilayers PLN exhibits ion channel activity with a low unitary conductance. From the effect of non-electrolyte polymers on this unitary conductance we estimate a narrow pore with a diameter of ca. 2.2 Å for this channel. This value is similar to that reported for the central pore in the structure of the PLN pentamer. Hence the PLN pentamer, which is in equilibrium with the monomer, is the most likely channel forming structure. Reconstituted PLN mutants, which either stabilize (K27A and R9C) or destabilize (I47A) the PLN pentamer and also phosphorylated PLN still generate the same unitary conductance of the wt/non-phosphorylated PLN. However the open probability of the phosphorylated PLN and of the R9C mutant is significantly lower than that of the respective wt/non-phosphorylated control. In the context of data on PLN/SERCA interaction and on Ca2+ accumulation in the sarcoplasmic reticulum the present results are consistent with the view that PLN channel activity could participate in the balancing of charge during Ca2+ uptake. A reduced total conductance of the K+ transporting PLN by phosphorylation or by the R9C mutation may stimulate Ca2+ uptake in the same way as an inhibition of K+ channels in the SR membrane. The R9C-PLN mutation, a putative cause of dilated cardiomyopathy, might hence affect SERCA activity also via its inherent low open probability.
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Affiliation(s)
| | - Andrea Saponaro
- Department of Biology and CNR IBF-Mi, Università degli Studi di Milano, Milano, Italy
| | - Howard S. Young
- Department of Biochemistry, University of Alberta, Edmonton, Canada
| | | | - Gerhard Thiel
- Plant Membrane Biophysics, TU-Darmstadt, Darmstadt, Germany
- * E-mail:
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11
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Maffeo C, Bhattacharya S, Yoo J, Wells D, Aksimentiev A. Modeling and simulation of ion channels. Chem Rev 2012; 112:6250-84. [PMID: 23035940 PMCID: PMC3633640 DOI: 10.1021/cr3002609] [Citation(s) in RCA: 148] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Christopher Maffeo
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - Swati Bhattacharya
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - Jejoong Yoo
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - David Wells
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
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12
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Liu J, Wolfe AJ, Eren E, Vijayaraghavan J, Indic M, van den Berg B, Movileanu L. Cation selectivity is a conserved feature in the OccD subfamily of Pseudomonas aeruginosa. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1818:2908-16. [PMID: 22824298 DOI: 10.1016/j.bbamem.2012.07.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2012] [Revised: 07/13/2012] [Accepted: 07/16/2012] [Indexed: 01/03/2023]
Abstract
To achieve the uptake of small, water-soluble nutrients, Pseudomonas aeruginosa, a pathogenic Gram-negative bacterium, employs substrate-specific channels located within its outer membrane. In this paper, we present a detailed description of the single-channel characteristics of six members of the outer membrane carboxylate channel D (OccD) subfamily. Recent structural studies showed that the OccD proteins share common features, such as a closely related, monomeric, 18-stranded β-barrel conformation and large extracellular loops, which are folded back into the channel lumen. Here, we report that the OccD proteins displayed single-channel activity with a unitary conductance covering an unusually broad range, between 20 and 670pS, as well as a diverse gating dynamics. Interestingly, we found that cation selectivity is a conserved trait among all members of the OccD subfamily, bringing a new distinction between the members of the OccD subfamily and the anion-selective OccK channels. Conserved cation selectivity of the OccD channels is in accord with an increased specificity and selectivity of these proteins for positively charged, carboxylate-containing substrates.
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Affiliation(s)
- Jiaming Liu
- Department of Physics, Syracuse University, Syracuse, NY 13244-1130, USA
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13
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Aschar-Sobbi R, Emmett TL, Kargacin GJ, Kargacin ME. Phospholamban phosphorylation increases the passive calcium leak from cardiac sarcoplasmic reticulum. Pflugers Arch 2012; 464:295-305. [DOI: 10.1007/s00424-012-1124-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Revised: 05/16/2012] [Accepted: 06/05/2012] [Indexed: 01/28/2023]
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14
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Gumbart J, Khalili-Araghi F, Sotomayor M, Roux B. Constant electric field simulations of the membrane potential illustrated with simple systems. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1818:294-302. [PMID: 22001851 DOI: 10.1016/j.bbamem.2011.09.030] [Citation(s) in RCA: 133] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Revised: 08/28/2011] [Accepted: 09/26/2011] [Indexed: 01/29/2023]
Abstract
Advances in modern computational methods and technology make it possible to carry out extensive molecular dynamics simulations of complex membrane proteins based on detailed atomic models. The ultimate goal of such detailed simulations is to produce trajectories in which the behavior of the system is as realistic as possible. A critical aspect that requires consideration in the case of biological membrane systems is the existence of a net electric potential difference across the membrane. For meaningful computations, it is important to have well validated methodologies for incorporating the latter in molecular dynamics simulations. A widely used treatment of the membrane potential in molecular dynamics consists of applying an external uniform electric field E perpendicular to the membrane. The field acts on all charged particles throughout the simulated system, and the resulting applied membrane potential V is equal to the applied electric field times the length of the periodic cell in the direction perpendicular to the membrane. A series of test simulations based on simple membrane-slab models are carried out to clarify the consequences of the applied field. These illustrative tests demonstrate that the constant-field method is a simple and valid approach for accounting for the membrane potential in molecular dynamics studies of biomolecular systems. This article is part of a Special Issue entitled: Membrane protein structure and function.
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Affiliation(s)
- James Gumbart
- Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
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15
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Structural topology of phospholamban pentamer in lipid bilayers by a hybrid solution and solid-state NMR method. Proc Natl Acad Sci U S A 2011; 108:9101-6. [PMID: 21576492 DOI: 10.1073/pnas.1016535108] [Citation(s) in RCA: 132] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Phospholamban (PLN) is a type II membrane protein that inhibits the sarcoplasmic reticulum Ca(2+)-ATPase (SERCA), thereby regulating calcium homeostasis in cardiac muscle. In membranes, PLN forms pentamers that have been proposed to function either as a storage for active monomers or as ion channels. Here, we report the T-state structure of pentameric PLN solved by a hybrid solution and solid-state NMR method. In lipid bilayers, PLN adopts a pinwheel topology with a narrow hydrophobic pore, which excludes ion transport. In the T state, the cytoplasmic amphipathic helices (domains Ia) are absorbed into the lipid bilayer with the transmembrane domains arranged in a left-handed coiled-coil configuration, crossing the bilayer with a tilt angle of approximately 11° with respect to the membrane normal. The tilt angle difference between the monomer and pentamer is approximately 13°, showing that intramembrane helix-helix association forces dominate over the hydrophobic mismatch, driving the overall topology of the transmembrane assembly. Our data reveal that both topology and function of PLN are shaped by the interactions with lipids, which fine-tune the regulation of SERCA.
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16
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Lian P, Wei DQ, Wang JF, Chou KC. An allosteric mechanism inferred from molecular dynamics simulations on phospholamban pentamer in lipid membranes. PLoS One 2011; 6:e18587. [PMID: 21525996 PMCID: PMC3078132 DOI: 10.1371/journal.pone.0018587] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2010] [Accepted: 03/10/2011] [Indexed: 11/18/2022] Open
Abstract
Phospholamban functions as a regulator of Ca(2+) concentration of cardiac muscle cells by triggering the bioactivity of sarcoplasmic reticulum Ca(2+)-ATPase. In order to understand its dynamic mechanism in the environment of bilayer surroundings, we performed long time-scale molecular dynamic simulations based on the high-resolution NMR structure of phospholamban pentamer. It was observed from the molecular dynamics trajectory analyses that the conformational transitions between the "bellflower" and "pinwheel" modes were detected for phospholamban. Particularly, the two modes became quite similar to each other after phospholamban was phosphorylated at Ser16. Based on these findings, an allosteric mechanism was proposed to elucidate the dynamic process of phospholamban interacting with Ca(2+)-ATPase.
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Affiliation(s)
- Peng Lian
- College of Life Science and Biotechnology and Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
- Key Laboratory of Systems Biomedicine, Ministry of Education, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Dong-Qing Wei
- College of Life Science and Biotechnology and Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
- Gordon Life Science Institute, San Diego, California, United States of America
- * E-mail: (DQW); (JFW)
| | - Jing-Fang Wang
- Key Laboratory of Systems Biomedicine, Ministry of Education, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Center for Bioinformation and Technology, Shanghai, China
- * E-mail: (DQW); (JFW)
| | - Kuo-Chen Chou
- Gordon Life Science Institute, San Diego, California, United States of America
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Smeazzetto S, Schröder I, Thiel G, Moncelli MR. Phospholamban generates cation selective ion channels. Phys Chem Chem Phys 2011; 13:12935-9. [DOI: 10.1039/c1cp20460b] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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