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Basu S, Assaf SS, Teheux F, Rooman M, Pucci F. BRANEart: Identify Stability Strength and Weakness Regions in Membrane Proteins. FRONTIERS IN BIOINFORMATICS 2021; 1:742843. [PMID: 36303753 PMCID: PMC9581023 DOI: 10.3389/fbinf.2021.742843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 11/03/2021] [Indexed: 11/22/2022] Open
Abstract
Understanding the role of stability strengths and weaknesses in proteins is a key objective for rationalizing their dynamical and functional properties such as conformational changes, catalytic activity, and protein-protein and protein-ligand interactions. We present BRANEart, a new, fast and accurate method to evaluate the per-residue contributions to the overall stability of membrane proteins. It is based on an extended set of recently introduced statistical potentials derived from membrane protein structures, which better describe the stability properties of this class of proteins than standard potentials derived from globular proteins. We defined a per-residue membrane propensity index from combinations of these potentials, which can be used to identify residues which strongly contribute to the stability of the transmembrane region or which would, on the contrary, be more stable in extramembrane regions, or vice versa. Large-scale application to membrane and globular proteins sets and application to tests cases show excellent agreement with experimental data. BRANEart thus appears as a useful instrument to analyze in detail the overall stability properties of a target membrane protein, to position it relative to the lipid bilayer, and to rationally modify its biophysical characteristics and function. BRANEart can be freely accessed from http://babylone.3bio.ulb.ac.be/BRANEart.
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Affiliation(s)
- Sankar Basu
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium
- Department of Microbiology, Austosh College, Under University of Calcutta, Kolkata, India
| | - Simon S. Assaf
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium
| | - Fabian Teheux
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium
| | - Marianne Rooman
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, Brussels, Belgium
- *Correspondence: Marianne Rooman, ; Fabrizio Pucci,
| | - Fabrizio Pucci
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, Brussels, Belgium
- *Correspondence: Marianne Rooman, ; Fabrizio Pucci,
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2
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Mravic M, Thomaston JL, Tucker M, Solomon PE, Liu L, DeGrado WF. Packing of apolar side chains enables accurate design of highly stable membrane proteins. Science 2019; 363:1418-1423. [PMID: 30923216 DOI: 10.1126/science.aav7541] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 02/28/2019] [Indexed: 12/21/2022]
Abstract
The features that stabilize the structures of membrane proteins remain poorly understood. Polar interactions contribute modestly, and the hydrophobic effect contributes little to the energetics of apolar side-chain packing in membranes. Disruption of steric packing can destabilize the native folds of membrane proteins, but is packing alone sufficient to drive folding in lipids? If so, then membrane proteins stabilized by this feature should be readily designed and structurally characterized-yet this has not been achieved. Through simulation of the natural protein phospholamban and redesign of variants, we define a steric packing code underlying its assembly. Synthetic membrane proteins designed using this code and stabilized entirely by apolar side chains conform to the intended fold. Although highly stable, the steric complementarity required for their folding is surprisingly stringent. Structural informatics shows that the designed packing motif recurs across the proteome, emphasizing a prominent role for precise apolar packing in membrane protein folding, stabilization, and evolution.
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Affiliation(s)
- Marco Mravic
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jessica L Thomaston
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Maxwell Tucker
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Paige E Solomon
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Lijun Liu
- State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China. .,DLX Scientific, Lawrence, KS 66049, USA
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.
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Cao Y, Wu X, Yang R, Wang X, Sun H, Lee I. Self-assembling study of sarcolipin and its mutants in multiple molecular dynamic simulations. Proteins 2017; 85:1065-1077. [PMID: 28241400 DOI: 10.1002/prot.25273] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 01/16/2017] [Accepted: 02/12/2017] [Indexed: 01/12/2023]
Abstract
The Sarcolipin (SLN) is a single trans-membrane protein that can self-assembly to dimer and oligomer for playing importantphysiological function. In this work, we addressed the dimerization of wild type SLN (wSLN) and its mutants (mSLNs) - I17A and I20A, using both coarse-grained (CG) and atomistic (AT) molecular dynamics (MD) simulations. Our results demonstrated that wSLN homodimer assembled as a left-handed helical complex, while mSLNs heterodimers assembled as right-handed complexes. Analysis of residue-residue contacts map indicated that isoleucine (Ile)-leucione (Leu) zipper domain played an important role in dimerization. The potential of mean force (PMF) demonstrated that wSLN homodimer was more stable than mSLNs heterodimers. Meanwhile, the mSLNs heterodimers preferred right-handed rather than left-handed helix. AT-MD simulations for wSLN and mSLNs were also in line with CG-MD simulations. These results provided the insights for understanding the mechanisms of SLNs self-assembling. Proteins 2017; 85:1065-1077. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Yipeng Cao
- School of Physics, Nankai University, 94 Weijin Road, Tianjin, 300071, P.R.China
| | - Xue Wu
- School of Physics, Nankai University, 94 Weijin Road, Tianjin, 300071, P.R.China
| | - Rui Yang
- School of Medicine, Nankai University, 94 Weijin Road, Tianjin, 300071, P.R.China
| | - Xinyu Wang
- School of Physics, Nankai University, 94 Weijin Road, Tianjin, 300071, P.R.China
| | - Haiying Sun
- School of Physics, Nankai University, 94 Weijin Road, Tianjin, 300071, P.R.China
| | - Imshik Lee
- School of Physics, Nankai University, 94 Weijin Road, Tianjin, 300071, P.R.China
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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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Mori T, Miyashita N, Im W, Feig M, Sugita Y. Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1635-51. [PMID: 26766517 DOI: 10.1016/j.bbamem.2015.12.032] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Revised: 12/24/2015] [Accepted: 12/29/2015] [Indexed: 12/15/2022]
Abstract
This paper reviews various enhanced conformational sampling methods and explicit/implicit solvent/membrane models, as well as their recent applications to the exploration of the structure and dynamics of membranes and membrane proteins. Molecular dynamics simulations have become an essential tool to investigate biological problems, and their success relies on proper molecular models together with efficient conformational sampling methods. The implicit representation of solvent/membrane environments is reasonable approximation to the explicit all-atom models, considering the balance between computational cost and simulation accuracy. Implicit models can be easily combined with replica-exchange molecular dynamics methods to explore a wider conformational space of a protein. Other molecular models and enhanced conformational sampling methods are also briefly discussed. As application examples, we introduce recent simulation studies of glycophorin A, phospholamban, amyloid precursor protein, and mixed lipid bilayers and discuss the accuracy and efficiency of each simulation model and method. 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)
- Takaharu Mori
- iTHES Research Group and Theoretical Molecular Science Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Naoyuki Miyashita
- Laboratory for Biomolecular Function Simulation, RIKEN Quantitative Biology Center, Integrated Innovation Building 7F, 6-7-1 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Faculty of Biology-Oriented Science and Technology, KINDAI University, 930 Nishimitani, Kinokawa, Wakayama 649-6493, Japan
| | - Wonpil Im
- Department of Molecular Sciences and Center for Computational Biology, The University of Kansas, 2030 Becker Drive, Lawrence, KS 66047, United States
| | - Michael Feig
- Laboratory for Biomolecular Function Simulation, RIKEN Quantitative Biology Center, Integrated Innovation Building 7F, 6-7-1 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, United States; Department of Chemistry, Michigan State University, East Lansing, MI 48824, United States
| | - Yuji Sugita
- iTHES Research Group and Theoretical Molecular Science Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Laboratory for Biomolecular Function Simulation, RIKEN Quantitative Biology Center, Integrated Innovation Building 7F, 6-7-1 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Department of Chemistry, Michigan State University, East Lansing, MI 48824, United States; Computational Biophysics Research Team, RIKEN Advanced Institute for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
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6
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Cao Y, Wu X, Lee I, Wang X. Molecular dynamics of water and monovalent-ions transportation mechanisms of pentameric sarcolipin. Proteins 2015; 84:73-81. [DOI: 10.1002/prot.24956] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 10/16/2015] [Accepted: 10/19/2015] [Indexed: 12/15/2022]
Affiliation(s)
- Yipeng Cao
- Institute of Physics, Nankai University; Tianjin China
| | - Xue Wu
- Institute of Physics, Nankai University; Tianjin China
| | - Imshik Lee
- Institute of Physics, Nankai University; Tianjin China
| | - Xinyu Wang
- Institute of Physics, Nankai University; Tianjin China
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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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8
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Sayadi M, Feig M. Role of conformational sampling of Ser16 and Thr17-phosphorylated phospholamban in interactions with SERCA. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1828:577-85. [PMID: 22959711 DOI: 10.1016/j.bbamem.2012.08.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2012] [Revised: 08/18/2012] [Accepted: 08/21/2012] [Indexed: 11/17/2022]
Abstract
Phosphorylation of phospholamban (PLB) at Ser16 and/ or Thr17 is believed to release its inhibitory effect on sarcoplasmic reticulum calcium ATPase. Ser16 phosphorylation of PLB has been suggested to cause a conformational change that alters the interaction between the enzyme and protein. Using computer simulations, the conformational sampling of Ser16 phosphorylated PLB in implicit membrane environment is compared here with the unphosphorylated PLB system to investigate these conformational changes. The results suggest that conformational changes in the cytoplasmic domain of PLB upon phosphorylation at Ser16 increase the likelihood of unfavorable interactions with SERCA in the E2 state prompting a conformational switch of SERCA from E2 to E1. Phosphorylation of PLB at Thr17 on the other hand does not appear to affect interactions with SERCA significantly suggesting that the mechanism of releasing the inhibitory effect is different between Thr17 phosphorylated and Ser16 phosphorylated PLB.
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Affiliation(s)
- Maryam Sayadi
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
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9
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Orłowski A, St-Pierre JF, Magarkar A, Bunker A, Pasenkiewicz-Gierula M, Vattulainen I, Róg T. Properties of the Membrane Binding Component of Catechol-O-methyltransferase Revealed by Atomistic Molecular Dynamics Simulations. J Phys Chem B 2011; 115:13541-50. [DOI: 10.1021/jp207177p] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Adam Orłowski
- Department of Computational Biophysics and Bioinformatics, Faculty of Biotechnology, Biochemistry and Biophysics, Jagiellonian University, Gronostajowa 7, Poland
- Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland
| | - Jean-François St-Pierre
- Departement de Physique and Regroupement Quebecois sur les Materiaux de Pointe, Universite de Montreal, C.P. 6128, Succursale Centre-ville, Montreal (Quebec), Canada
| | - Aniket Magarkar
- Centre for Drug Research, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014, University of Helsinki, Finland
| | - Alex Bunker
- Centre for Drug Research, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014, University of Helsinki, Finland
- Department of Chemistry, Aalto University School of Science, P.O. Box 6100, FI-02015, AALTO, Espoo, Finland
| | - Marta Pasenkiewicz-Gierula
- Department of Computational Biophysics and Bioinformatics, Faculty of Biotechnology, Biochemistry and Biophysics, Jagiellonian University, Gronostajowa 7, Poland
| | - Ilpo Vattulainen
- Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland
- Department of Applied Physics, Aalto University School of Science, Finland
- MEMPHYS−Center for Biomembrane Physics, University of Southern Denmark, Odense, Denmark
| | - Tomasz Róg
- Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland
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10
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Im W, Jo S, Kim T. An ensemble dynamics approach to decipher solid-state NMR observables of membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1818:252-62. [PMID: 21851810 DOI: 10.1016/j.bbamem.2011.07.048] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Revised: 07/22/2011] [Accepted: 07/30/2011] [Indexed: 11/18/2022]
Abstract
Solid-state NMR (SSNMR) is an invaluable tool for determining orientations of membrane proteins and peptides in lipid bilayers. Such orientational descriptions provide essential information about membrane protein functions. However, when a semi-static single conformer model is used to interpret various SSNMR observables, important dynamics information can be missing, and, sometimes, even orientational information can be misinterpreted. In addition, over the last decade, molecular dynamics (MD) simulation and semi-static SSNMR interpretation have shown certain levels of discrepancies in terms of transmembrane helix orientation and dynamics. Dynamic fitting models have recently been proposed to resolve these discrepancies by taking into account transmembrane helix whole body motions using additional parameters. As an alternative approach, we have developed SSNMR ensemble dynamics (SSNMR-ED) using multiple conformer models, which generates an ensemble of structures that satisfies the experimental observables without any fitting parameters. In this review, various computational methods for determining transmembrane helix orientations are discussed, and the distributions of VpuTM (from HIV-1) and WALP23 (a synthetic peptide) orientations from SSNMR-ED simulations are compared with those from MD simulations and semi-static/dynamic fitting models. Such comparisons illustrate that SSNMR-ED can be used as a general means to extract both membrane protein structure and dynamics from the SSNMR measurements. This article is part of a Special Issue entitled: Membrane protein structure and function.
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Affiliation(s)
- Wonpil Im
- Department of Molecular Biosciences and Center for Bioinformatics, The University of Kansas, 2030 Becker Drive, Lawrence, KS 66047, USA.
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Haizlip KM, Janssen PML. In vitro studies of early cardiac remodeling: impact on contraction and calcium handling. Front Biosci (Schol Ed) 2011; 3:1047-57. [PMID: 21622254 DOI: 10.2741/209] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Cardiac remodeling, hypertrophy, and alterations in calcium signaling are changes of the heart that often lead to failure. After a hypertrophic stimulus, the heart progresses through a state of compensated hypertrophy which over time leads to decompensated hypertrophy or failure. It is at this point that a cardiac transplant is required for survival making early detection imperative. Current experimental systems used to study the remodeling of the heart include in vivo systems (the whole body), isolated organ and sub-organ tissue, and the individual cardiac muscle cells and organelles.. During pathological remodeling there is a derangement in the intracellular calcium handling processes. These derangements are thought to lead to a dysregulation of contractile output. Hence, understanding the mechanism between remodeling and dysregulation is of great interest in the cardiac field and will ultimately help in the development of future treatment and early detection. This review will center on changes in contraction and calcium handling in early cardiac remodeling, with a specific focus on findings in two different in vitro model systems: multicellular and individual cell preparations.
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Affiliation(s)
- Kaylan M Haizlip
- Department of Physiology and Cell Biology, College of Medicine, The Ohio State University, Columbus, OH 43210-1218, USA
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12
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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: 143] [Impact Index Per Article: 11.0] [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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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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14
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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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15
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Manna M, Mukhopadhyay C. Cholesterol driven alteration of the conformation and dynamics of phospholamban in model membranes. Phys Chem Chem Phys 2011; 13:20188-98. [DOI: 10.1039/c1cp21793c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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16
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Sayadi M, Tanizaki S, Feig M. Effect of membrane thickness on conformational sampling of phospholamban from computer simulations. Biophys J 2010; 98:805-14. [PMID: 20197034 DOI: 10.1016/j.bpj.2009.11.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2009] [Revised: 10/31/2009] [Accepted: 11/09/2009] [Indexed: 10/19/2022] Open
Abstract
The conformational sampling of monomeric, membrane-bound phospholamban is described from computer simulations. Phospholamban (PLB) plays a key role as a regulator of sarcoplasmic reticulum calcium ATPase. An implicit membrane model is used in conjunction with replica exchange molecular dynamics simulations to reach mus-ms timescales. The implicit membrane model was also used to study the effect of different membrane thicknesses by scaling the low-dielectric region. The conformational sampling with the membrane model mimicking dipalmitoylphosphatidylcholine bilayers is in good agreement overall with experimental measurements, but consists of a wide variety of different conformations including structures not described previously. The conformational ensemble shifts significantly in the presence of thinner or thicker membranes. This has implications for the structure and dynamics of PLB in physiological membranes and offers what we believe to be a new interpretation of previous experimental measurements of PLB in detergents and microsomal membrane.
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Affiliation(s)
- Maryam Sayadi
- Department of Chemistry, Michigan State University, East Lansing, USA
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17
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Maffeo C, Aksimentiev A. Structure, dynamics, and ion conductance of the phospholamban pentamer. Biophys J 2009; 96:4853-65. [PMID: 19527644 DOI: 10.1016/j.bpj.2009.03.053] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2008] [Revised: 03/12/2009] [Accepted: 03/20/2009] [Indexed: 11/19/2022] Open
Abstract
A 52-residue membrane protein, phospholamban (PLN) is an inhibitor of an adenosine-5'-triphosphate-driven calcium pump, the Ca2+-ATPase. Although the inhibition of Ca2+-ATPase involves PLN monomers, in a lipid bilayer membrane, PLN monomers form stable pentamers of unknown biological function. The recent NMR structure of a PLN pentamer depicts cytoplasmic helices extending normal to the bilayer in what is known as the bellflower conformation. The structure shows transmembrane helices forming a hydrophobic pore 4 A in diameter, which is reminiscent of earlier reports of possible ion conductance through PLN pentamers. However, recent FRET measurements suggested an alternative structure for the PLN pentamer, known as the pinwheel model, which features a narrower transmembrane pore and cytoplasmic helices that lie against the bilayer. Here, we report on structural dynamics and conductance properties of the PLN pentamers from all-atom (AA) and coarse-grained (CG) molecular dynamics simulations. Our AA simulations of the bellflower model demonstrate that in a lipid bilayer membrane or a detergent micelle, the cytoplasmic helices undergo large structural fluctuations, whereas the transmembrane pore shrinks and becomes asymmetric. Similar asymmetry of the transmembrane region was observed in the AA simulations of the pinwheel model; the cytoplasmic helices remained in contact with the bilayer. Using the CG approach, structural dynamics of both models were investigated on a microsecond timescale. The cytoplasmic helices of the CG bellflower model were observed to fall against the bilayer, whereas in the CG pinwheel model the conformation of the cytoplasmic helices remained stable. Using steered molecular dynamics simulations, we investigated the feasibility of ion conductance through the pore of the bellflower model. The resulting approximate potentials of mean force indicate that the PLN pentamer is unlikely to function as an ion channel.
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Affiliation(s)
- Christopher Maffeo
- Department of Physics, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA
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On the function of pentameric phospholamban: ion channel or storage form? Biophys J 2009; 96:L60-2. [PMID: 19450461 DOI: 10.1016/j.bpj.2009.03.013] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2008] [Revised: 02/24/2009] [Accepted: 03/04/2009] [Indexed: 11/22/2022] Open
Abstract
Phospholamban (PLN) is an integral membrane protein that inhibits the sarcoplasmic reticulum Ca(2+)-ATPase, thereby regulating muscle contractility. We report a combined electrochemical and theoretical study demonstrating that the pentameric PLN does not possess channel activity for conducting chloride or calcium ions across the lipid membrane. This suggests that the pentameric configuration of PLN primarily serves as a storage form for the regulatory function of muscle relaxation by the PLN monomer.
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