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Postic G, Ghouzam Y, Guiraud V, Gelly JC. Membrane positioning for high- and low-resolution protein structures through a binary classification approach. Protein Eng Des Sel 2015; 29:87-91. [PMID: 26685702 DOI: 10.1093/protein/gzv063] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 11/08/2015] [Indexed: 11/13/2022] Open
Abstract
The critical importance of algorithms for orienting proteins in the lipid bilayer stems from the extreme difficulty in obtaining experimental data about the membrane boundaries. Here, we present a computational method for positioning protein structures in the membrane, based on the sole alpha carbon coordinates and, therefore, compatible with both high and low structural resolutions. Our algorithm follows a new and simple approach, by treating the membrane assignment problem as a binary classification. Compared with the state-of-the-art algorithms, our method achieves similar accuracy, while being faster. Finally, our open-source software is also capable of processing coarse-grained models of protein structures.
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Affiliation(s)
- Guillaume Postic
- Inserm U1134, Paris, France Univ. Paris Diderot, Sorbonne Paris Cité, UMR_S 1134, Paris, France Institut National de la Transfusion Sanguine, Paris, France Laboratory of Excellence GR-Ex, Paris, France
| | - Yassine Ghouzam
- Inserm U1134, Paris, France Univ. Paris Diderot, Sorbonne Paris Cité, UMR_S 1134, Paris, France Institut National de la Transfusion Sanguine, Paris, France Laboratory of Excellence GR-Ex, Paris, France
| | - Vincent Guiraud
- Inserm U1134, Paris, France Univ. Paris Diderot, Sorbonne Paris Cité, UMR_S 1134, Paris, France Institut National de la Transfusion Sanguine, Paris, France Laboratory of Excellence GR-Ex, Paris, France
| | - Jean-Christophe Gelly
- Inserm U1134, Paris, France Univ. Paris Diderot, Sorbonne Paris Cité, UMR_S 1134, Paris, France Institut National de la Transfusion Sanguine, Paris, France Laboratory of Excellence GR-Ex, Paris, France
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52
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Dyrka W, Kurczyńska M, Konopka BM, Kotulska M. Fast assessment of structural models of ion channels based on their predicted current-voltage characteristics. Proteins 2015; 84:217-31. [PMID: 26650347 DOI: 10.1002/prot.24967] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 11/19/2015] [Accepted: 11/29/2015] [Indexed: 11/11/2022]
Abstract
Computational prediction of protein structures is a difficult task, which involves fast and accurate evaluation of candidate model structures. We propose to enhance single-model quality assessment with a functionality evaluation phase for proteins whose quantitative functional characteristics are known. In particular, this idea can be applied to evaluation of structural models of ion channels, whose main function - conducting ions - can be quantitatively measured with the patch-clamp technique providing the current-voltage characteristics. The study was performed on a set of KcsA channel models obtained from complete and incomplete contact maps. A fast continuous electrodiffusion model was used for calculating the current-voltage characteristics of structural models. We found that the computed charge selectivity and total current were sensitive to structural and electrostatic quality of models. In practical terms, we show that evaluating predicted conductance values is an appropriate method to eliminate models with an occluded pore or with multiple erroneously created pores. Moreover, filtering models on the basis of their predicted charge selectivity results in a substantial enrichment of the candidate set in highly accurate models. Tests on three other ion channels indicate that, in addition to being a proof of the concept, our function-oriented single-model quality assessment method can be directly applied to evaluation of structural models of some classes of protein channels. Finally, our work raises an important question whether a computational validation of functionality should be included in the evaluation process of structural models, whenever possible.
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Affiliation(s)
- Witold Dyrka
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Technology, Wybrzeze Wyspianskiego 27, Wroclaw, 50-370, Poland
| | - Monika Kurczyńska
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Technology, Wybrzeze Wyspianskiego 27, Wroclaw, 50-370, Poland
| | - Bogumił M Konopka
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Technology, Wybrzeze Wyspianskiego 27, Wroclaw, 50-370, Poland
| | - Małgorzata Kotulska
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Technology, Wybrzeze Wyspianskiego 27, Wroclaw, 50-370, Poland
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53
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Advances in Computational Techniques to Study GPCR–Ligand Recognition. Trends Pharmacol Sci 2015; 36:878-890. [DOI: 10.1016/j.tips.2015.08.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 07/15/2015] [Accepted: 08/07/2015] [Indexed: 12/16/2022]
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54
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Blees A, Reichel K, Trowitzsch S, Fisette O, Bock C, Abele R, Hummer G, Schäfer LV, Tampé R. Assembly of the MHC I peptide-loading complex determined by a conserved ionic lock-switch. Sci Rep 2015; 5:17341. [PMID: 26611325 PMCID: PMC4661472 DOI: 10.1038/srep17341] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 10/15/2015] [Indexed: 01/14/2023] Open
Abstract
Salt bridges in lipid bilayers play a decisive role in the dynamic assembly and downstream signaling of the natural killer and T-cell receptors. Here, we describe the identification of an inter-subunit salt bridge in the membrane within yet another key component of the immune system, the peptide-loading complex (PLC). The PLC regulates cell surface presentation of self-antigens and antigenic peptides via molecules of the major histocompatibility complex class I. We demonstrate that a single salt bridge in the membrane between the transporter associated with antigen processing TAP and the MHC I-specific chaperone tapasin is essential for the assembly of the PLC and for efficient MHC I antigen presentation. Molecular modeling and all-atom molecular dynamics simulations suggest an ionic lock-switch mechanism for the binding of TAP to tapasin, in which an unfavorable uncompensated charge in the ER-membrane is prevented through complex formation. Our findings not only deepen the understanding of the interaction network within the PLC, but also provide evidence for a general interaction principle of dynamic multiprotein membrane complexes in immunity.
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Affiliation(s)
- Andreas Blees
- Institute of Biochemistry, Biocenter, Goethe-University Frankfurt am Main, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Katrin Reichel
- Lehrstuhl für Theoretische Chemie, Ruhr-University Bochum, D-44780 Bochum, Germany
- Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, D-60438 Frankfurt am Main, Germany
| | - Simon Trowitzsch
- Institute of Biochemistry, Biocenter, Goethe-University Frankfurt am Main, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Olivier Fisette
- Lehrstuhl für Theoretische Chemie, Ruhr-University Bochum, D-44780 Bochum, Germany
| | - Christoph Bock
- Institute of Biochemistry, Biocenter, Goethe-University Frankfurt am Main, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Rupert Abele
- Institute of Biochemistry, Biocenter, Goethe-University Frankfurt am Main, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Gerhard Hummer
- Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, D-60438 Frankfurt am Main, Germany
| | - Lars V. Schäfer
- Lehrstuhl für Theoretische Chemie, Ruhr-University Bochum, D-44780 Bochum, Germany
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe-University Frankfurt am Main, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
- Cluster of Excellence–Macromolecular Complexes, Goethe-University Frankfurt am Main, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
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55
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Determining the N-terminal orientations of recombinant transmembrane proteins in the Escherichia coli plasma membrane. Sci Rep 2015; 5:15086. [PMID: 26462555 PMCID: PMC4604451 DOI: 10.1038/srep15086] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 09/11/2015] [Indexed: 11/08/2022] Open
Abstract
In silico algorithms have been the common approach for transmembrane (TM) protein topology prediction. However, computational tools may produce questionable results and experimental validation has proven difficult. Although biochemical strategies are available to determine the C-terminal orientation of TM proteins, experimental strategies to determine the N-terminal orientation are still limited but needed because the N-terminal end is essential for membrane targeting. Here, we describe a new and easy method to effectively determine the N-terminal orientation of the target TM proteins in Escherichia coli plasma membrane environment. D94N, the mutant of bacteriorhodopsin from Haloarcula marismortui, can be a fusion partner to increase the production of the target TM proteins if their N-termini are in cytoplasm (Nin orientation). To create a suitable linker for orientating the target TM proteins with the periplasmic N-termini (Nout orientation) correctly, we designed a three-TM-helix linker fused at the C-terminus of D94N fusion partner (termed D94N-3TM) and found that D94N-3TM can specifically improve the production of the Nout target TM proteins. In conclusion, D94N and D94N-3TM fusion partners can be applied to determine the N-terminal end of the target TM proteins oriented either Nin or Nout by evaluating the net expression of the fusion proteins.
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56
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An empirical energy function for structural assessment of protein transmembrane domains. Biochimie 2015; 115:155-61. [DOI: 10.1016/j.biochi.2015.05.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 05/21/2015] [Indexed: 11/19/2022]
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57
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Stansfeld PJ, Goose JE, Caffrey M, Carpenter EP, Parker JL, Newstead S, Sansom MSP. MemProtMD: Automated Insertion of Membrane Protein Structures into Explicit Lipid Membranes. Structure 2015; 23:1350-61. [PMID: 26073602 PMCID: PMC4509712 DOI: 10.1016/j.str.2015.05.006] [Citation(s) in RCA: 167] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 04/24/2015] [Accepted: 05/02/2015] [Indexed: 01/26/2023]
Abstract
There has been exponential growth in the number of membrane protein structures determined. Nevertheless, these structures are usually resolved in the absence of their lipid environment. Coarse-grained molecular dynamics (CGMD) simulations enable insertion of membrane proteins into explicit models of lipid bilayers. We have automated the CGMD methodology, enabling membrane protein structures to be identified upon their release into the PDB and embedded into a membrane. The simulations are analyzed for protein-lipid interactions, identifying lipid binding sites, and revealing local bilayer deformations plus molecular access pathways within the membrane. The coarse-grained models of membrane protein/bilayer complexes are transformed to atomistic resolution for further analysis and simulation. Using this automated simulation pipeline, we have analyzed a number of recently determined membrane protein structures to predict their locations within a membrane, their lipid/protein interactions, and the functional implications of an enhanced understanding of the local membrane environment of each protein. A simulation pipeline for predicting the location of a membrane protein in a bilayer A protocol for identifying novel membrane protein structures in the PDB Analysis of lipid binding sites and local bilayer deformation by membrane proteins Functional implications from enhanced understanding of local membrane environments
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Affiliation(s)
- Phillip J Stansfeld
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Joseph E Goose
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Martin Caffrey
- Schools of Medicine and Biochemistry & Immunology, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Elisabeth P Carpenter
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Joanne L Parker
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Simon Newstead
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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58
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H. DeLuca S, L. DeLuca S, Leaver-Fay A, Meiler J. RosettaTMH: a method for membrane protein structure elucidation combining EPR distance restraints with assembly of transmembrane helices. AIMS BIOPHYSICS 2015. [DOI: 10.3934/biophy.2016.1.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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59
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Abstract
Recent advances in identifying residue-residue contacts from large multiple sequence alignments have enabled impressive gains to be made in the field of protein structure prediction. In this chapter, we discuss these advances and provide a step-by-step guide to applying the latest tools to the de novo modelling of alpha-helical transmembrane proteins. As a practical example, we demonstrate the process of building an accurate 3D model of a G protein-coupled receptor, correctly orientated in the membrane, using only its primary protein sequence.
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Affiliation(s)
- Timothy Nugent
- Bioinformatics Group, Department of Computer Science, University College London, Office: 8.11, Desk: 206, Gower Street, London, WC1E 6BT, UK,
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60
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Zhu F, Clauss M. Evaluating membrane affinity by integrating protein orientations. J Mol Graph Model 2014; 54:141-7. [PMID: 25459766 DOI: 10.1016/j.jmgm.2014.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 09/13/2014] [Accepted: 10/15/2014] [Indexed: 11/16/2022]
Abstract
Energetic interactions of a protein with lipid bilayers determine its propensity to reside in the membrane. Here we seek to evaluate the membrane interactions for EMAPII, a protein found to be released from the cell by unknown mechanisms, as well as several other proteins. Using a knowledge-based coarse-grained membrane potential, we calculate the free energy profiles for these proteins by integrating out the orientation degrees of freedom. Due to the invariance of energy under in-plane rotations about the membrane normal, the orientation space can be reduced to two dimensions and mapped onto the surface of a unit sphere, thus making visualization, sampling and integration more convenient. The integrated free energy profiles determine the relative probabilities along the membrane normal for the proteins regardless of their orientations, and display distinctive characteristics for membrane proteins and water-soluble proteins. The membrane interactions for EMAPII exhibit typical features of a water-soluble protein, with a high energetic barrier to enter or cross the membrane. Our results thus suggest that similar to the non-classical export of FGF1, the release of EMAPII would involve more complicated mechanisms than simple passive diffusion across the membrane.
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Affiliation(s)
- Fangqiang Zhu
- Department of Physics, Indiana University - Purdue University Indianapolis, United States.
| | - Matthias Clauss
- Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Indianapolis, IN, United States
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61
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Tan J, Rouse SL, Li D, Pye VE, Vogeley L, Brinth AR, El Arnaout T, Whitney JC, Howell PL, Sansom MSP, Caffrey M. A conformational landscape for alginate secretion across the outer membrane of Pseudomonas aeruginosa. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:2054-68. [PMID: 25084326 PMCID: PMC4118822 DOI: 10.1107/s1399004714001850] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 01/26/2014] [Indexed: 11/11/2022]
Abstract
The exopolysaccharide alginate is an important component of biofilms produced by Pseudomonas aeruginosa, a major pathogen that contributes to the demise of cystic fibrosis patients. Alginate exits the cell via the outer membrane porin AlgE. X-ray structures of several AlgE crystal forms are reported here. Whilst all share a common β-barrel constitution, they differ in the degree to which loops L2 and T8 are ordered. L2 and T8 have been identified as an extracellular gate (E-gate) and a periplasmic gate (P-gate), respectively, that reside on either side of an alginate-selectivity pore located midway through AlgE. Passage of alginate across the membrane is proposed to be regulated by the sequential opening and closing of the two gates. In one crystal form, the selectivity pore contains a bound citrate. Because citrate mimics the uronate monomers of alginate, its location is taken to highlight a route through AlgE taken by alginate as it crosses the pore. Docking and molecular-dynamics simulations support and extend the proposed transport mechanism. Specifically, the P-gate and E-gate are flexible and move between open and closed states. Citrate can leave the selectivity pore bidirectionally. Alginate docks stably in a linear conformation through the open pore. To translate across the pore, a force is required that presumably is provided by the alginate-synthesis machinery. Accessing the open pore is facilitated by complex formation between AlgE and the periplasmic protein AlgK. Alginate can thread through a continuous pore in the complex, suggesting that AlgK pre-orients newly synthesized exopolysaccharide for delivery to AlgE.
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Affiliation(s)
- Jingquan Tan
- Schools of Medicine and Biochemistry and Immunology, Trinity College, Dublin, Ireland
| | - Sarah L. Rouse
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, England
| | - Dianfan Li
- Schools of Medicine and Biochemistry and Immunology, Trinity College, Dublin, Ireland
| | - Valerie E. Pye
- Schools of Medicine and Biochemistry and Immunology, Trinity College, Dublin, Ireland
| | - Lutz Vogeley
- Schools of Medicine and Biochemistry and Immunology, Trinity College, Dublin, Ireland
| | - Alette R. Brinth
- Schools of Medicine and Biochemistry and Immunology, Trinity College, Dublin, Ireland
| | - Toufic El Arnaout
- Schools of Medicine and Biochemistry and Immunology, Trinity College, Dublin, Ireland
| | - John C. Whitney
- Program in Molecular Structure and Function, The Hospital for Sick Children, Toronto, Ontario, Canada
- University of Toronto, Toronto, Ontario, Canada
| | - P. Lynne Howell
- Program in Molecular Structure and Function, The Hospital for Sick Children, Toronto, Ontario, Canada
- University of Toronto, Toronto, Ontario, Canada
| | - Mark S. P. Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, England
| | - Martin Caffrey
- Schools of Medicine and Biochemistry and Immunology, Trinity College, Dublin, Ireland
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