1
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Marinelli F, Faraldo-Gómez JD. Conformational free-energy landscapes of a Na +/Ca 2+ exchanger explain its alternating-access mechanism and functional specificity. Proc Natl Acad Sci U S A 2024; 121:e2318009121. [PMID: 38588414 PMCID: PMC11032461 DOI: 10.1073/pnas.2318009121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 02/20/2024] [Indexed: 04/10/2024] Open
Abstract
Secondary-active transporters catalyze the movement of myriad substances across all cellular membranes, typically against opposing concentration gradients, and without consuming any ATP. To do so, these proteins employ an intriguing structural mechanism evolved to be activated only upon recognition or release of the transported species. We examine this self-regulated mechanism using a homolog of the cardiac Na+/Ca2+ exchanger as a model system. Using advanced computer simulations, we map out the complete functional cycle of this transporter, including unknown conformations that we validate against existing experimental data. Calculated free-energy landscapes reveal why this transporter functions as an antiporter rather than a symporter, why it specifically exchanges Na+ and Ca2+, and why the stoichiometry of this exchange is exactly 3:1. We also rationalize why the protein does not exchange H+ for either Ca2+ or Na+, despite being able to bind H+ and its high similarity with H+/Ca2+ exchangers. Interestingly, the nature of this transporter is not explained by its primary structural states, known as inward- and outward-open conformations; instead, the defining factor is the feasibility of conformational intermediates between those states, wherein access pathways leading to the substrate binding sites become simultaneously occluded from both sides of the membrane. This analysis offers a physically coherent, broadly transferable route to understand the emergence of function from structure among secondary-active membrane transporters.
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Affiliation(s)
- Fabrizio Marinelli
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, NIH, Bethesda, MD20814
| | - José D. Faraldo-Gómez
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, NIH, Bethesda, MD20814
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2
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Hacisuleyman A, Erman B. Fine tuning rigid body docking results using the Dreiding force field: A computational study of 36 known nanobody-protein complexes. Proteins 2023; 91:1417-1426. [PMID: 37232507 DOI: 10.1002/prot.26529] [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: 01/19/2023] [Revised: 05/03/2023] [Accepted: 05/08/2023] [Indexed: 05/27/2023]
Abstract
This paper aims to understand the binding strategies of a nanobody-protein pair by studying known complexes. Rigid body protein-ligand docking programs produce several complexes, called decoys, which are good candidates with high scores of shape complementarity, electrostatic interactions, desolvation, buried surface area, and Lennard-Jones potentials. However, the decoy that corresponds to the native structure is not known. We studied 36 nanobody-protein complexes from the single domain antibody database, sd-Ab DB, http://www.sdab-db.ca/. For each structure, a large number of decoys are generated using the Fast Fourier Transform algorithm of the software ZDOCK. The decoys were ranked according to their target protein-nanobody interaction energies, calculated by using the Dreiding Force Field, with rank 1 having the lowest interaction energy. Out of 36 protein data bank (PDB) structures, 25 true structures were predicted as rank 1. Eleven of the remaining structures required Ångstrom size rigid body translations of the nanobody relative to the protein to match the given PDB structure. After the translation, the Dreiding interaction (DI) energies of all complexes decreased and became rank 1. In one case, rigid body rotations as well as translations of the nanobody were required for matching the crystal structure. We used a Monte Carlo algorithm that randomly translates and rotates the nanobody of a decoy and calculates the DI energy. Results show that rigid body translations and the DI energy are sufficient for determining the correct binding location and pose of ZDOCK created decoys. A survey of the sd-Ab DB showed that each nanobody makes at least one salt bridge with its partner protein, indicating that salt bridge formation is an essential strategy in nanobody-protein recognition. Based on the analysis of the 36 crystal structures and evidence from existing literature, we propose a set of principles that could be used in the design of nanobodies.
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Affiliation(s)
- Aysima Hacisuleyman
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Burak Erman
- Chemical and Biological Engineering, Koc University, Istanbul, Turkey
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3
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Katsube S, Willibal K, Vemulapally S, Hariharan P, Tikhonova E, Pardon E, Kaback HR, Steyaert J, Guan L. In vivo and in vitro characterizations of melibiose permease (MelB) conformation-dependent nanobodies reveal sugar-binding mechanisms. J Biol Chem 2023; 299:104967. [PMID: 37380079 PMCID: PMC10374971 DOI: 10.1016/j.jbc.2023.104967] [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: 02/13/2023] [Revised: 06/13/2023] [Accepted: 06/19/2023] [Indexed: 06/30/2023] Open
Abstract
Salmonella enterica serovar Typhimurium melibiose permease (MelBSt) is a prototype of the Na+-coupled major facilitator superfamily transporters, which are important for the cellular uptake of molecules including sugars and small drugs. Although the symport mechanisms have been well-studied, mechanisms of substrate binding and translocation remain enigmatic. We have previously determined the sugar-binding site of outward-facing MelBSt by crystallography. To obtain other key kinetic states, here we raised camelid single-domain nanobodies (Nbs) and carried out a screening against the WT MelBSt under 4 ligand conditions. We applied an in vivo cAMP-dependent two-hybrid assay to detect interactions of Nbs with MelBSt and melibiose transport assays to determine the effects on MelBSt functions. We found that all selected Nbs showed partial to complete inhibitions of MelBSt transport activities, confirming their intracellular interactions. A group of Nbs (714, 725, and 733) was purified, and isothermal titration calorimetry measurements showed that their binding affinities were significantly inhibited by the substrate melibiose. When titrating melibiose to the MelBSt/Nb complexes, Nb also inhibited the sugar-binding. However, the Nb733/MelBSt complex retained binding to the coupling cation Na+ and also to the regulatory enzyme EIIAGlc of the glucose-specific phosphoenolpyruvate/sugar phosphotransferase system. Further, EIIAGlc/MelBSt complex also retained binding to Nb733 and formed a stable supercomplex. All data indicated that MelBSt trapped by Nbs retained its physiological functions and the trapped conformation is similar to that bound by the physiological regulator EIIAGlc. Therefore, these conformational Nbs can be useful tools for further structural, functional, and conformational analyses.
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Affiliation(s)
- Satoshi Katsube
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas, USA
| | - Katleen Willibal
- VIB Center for Structural Biology Research, VIB, Brussel, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, Brussel, Belgium
| | - Sangama Vemulapally
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas, USA
| | - Parameswaran Hariharan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas, USA
| | - Elena Tikhonova
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas, USA
| | - Els Pardon
- VIB Center for Structural Biology Research, VIB, Brussel, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, Brussel, Belgium
| | - H Ronald Kaback
- Department of Physiology and Department of Microbiology, Immunology, and Molecular Genetics, Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California, USA
| | - Jan Steyaert
- VIB Center for Structural Biology Research, VIB, Brussel, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, Brussel, Belgium
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas, USA.
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4
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Utilization of AlphaFold2 to Predict MFS Protein Conformations after Selective Mutation. Int J Mol Sci 2022; 23:ijms23137235. [PMID: 35806248 PMCID: PMC9266783 DOI: 10.3390/ijms23137235] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 06/23/2022] [Accepted: 06/26/2022] [Indexed: 02/05/2023] Open
Abstract
The major facilitator superfamily (MFS) is the largest secondary transporter family and is responsible for transporting a broad range of substrates across the biomembrane. These proteins are involved in a series of conformational changes during substrate transport. To decipher the transport mechanism, it is necessary to obtain structures of these different conformations. At present, great progress has been made in predicting protein structure based on coevolutionary information. In this study, AlphaFold2 was used to predict different conformational structures for 69 MFS transporters of E. coli after the selective mutation of residues at the interface between the N- and C-terminal domains. The predicted structures for these mutants had small RMSD values when compared to structures obtained using X-ray crystallography, which indicates that AlphaFold2 predicts the structure of MSF transporters with high accuracy. In addition, different conformations of other transporter family proteins have been successfully predicted based on mutation methods. This study provides a structural basis to study the transporting mechanism of the MFS transporters and a method to probe dynamic conformation changes of transporter family proteins when performing their function.
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5
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Matsuzaki Y, Kajiwara K, Aoki W, Ueda M. Production of Single-Domain Antibodies in Pichia pastoris. Methods Mol Biol 2022; 2446:181-203. [PMID: 35157274 DOI: 10.1007/978-1-0716-2075-5_9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Single-domain antibodies (sdAbs) are binders that consist of a single immunoglobulin domain. SdAbs have gained importance as therapeutics, diagnostic reagents, and research tools. Functional sdAbs are commonly produced in Escherichia coli, which is a simple and widely used host for production of recombinant proteins. However, there are drawbacks of the E. coli expression system, including the potential for misfolded recombinant proteins and pyrogenic contamination with toxic lipopolysaccharides. Pichia pastoris is an alternative host for the production of heterologous proteins because of its high recombinant protein yields and the ability to produce soluble, properly folded proteins without lipopolysaccharide contamination. Here, we describe a method to produce sdAbs in P. pastoris. We present methods for the cloning of sdAb-encoding genes into a P. pastoris expression vector, production and purification of sdAbs, and measurement of sdAb-binding kinetics. Functional sdAbs are easily and routinely obtained using these methods.
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Affiliation(s)
- Yusei Matsuzaki
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Kaho Kajiwara
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Wataru Aoki
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
- Core Research for Evolutionary Science and Technology (CREST), Japan Science and Technology Agency (JST), Tokyo, Japan
| | - Mitsuyoshi Ueda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan.
- Core Research for Evolutionary Science and Technology (CREST), Japan Science and Technology Agency (JST), Tokyo, Japan.
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6
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Drew D, North RA, Nagarathinam K, Tanabe M. Structures and General Transport Mechanisms by the Major Facilitator Superfamily (MFS). Chem Rev 2021; 121:5289-5335. [PMID: 33886296 PMCID: PMC8154325 DOI: 10.1021/acs.chemrev.0c00983] [Citation(s) in RCA: 165] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Indexed: 12/12/2022]
Abstract
The major facilitator superfamily (MFS) is the largest known superfamily of secondary active transporters. MFS transporters are responsible for transporting a broad spectrum of substrates, either down their concentration gradient or uphill using the energy stored in the electrochemical gradients. Over the last 10 years, more than a hundred different MFS transporter structures covering close to 40 members have provided an atomic framework for piecing together the molecular basis of their transport cycles. Here, we summarize the remarkable promiscuity of MFS members in terms of substrate recognition and proton coupling as well as the intricate gating mechanisms undergone in achieving substrate translocation. We outline studies that show how residues far from the substrate binding site can be just as important for fine-tuning substrate recognition and specificity as those residues directly coordinating the substrate, and how a number of MFS transporters have evolved to form unique complexes with chaperone and signaling functions. Through a deeper mechanistic description of glucose (GLUT) transporters and multidrug resistance (MDR) antiporters, we outline novel refinements to the rocker-switch alternating-access model, such as a latch mechanism for proton-coupled monosaccharide transport. We emphasize that a full understanding of transport requires an elucidation of MFS transporter dynamics, energy landscapes, and the determination of how rate transitions are modulated by lipids.
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Affiliation(s)
- David Drew
- Department
of Biochemistry and Biophysics, Stockholm
University, SE 106 91 Stockholm, Sweden
| | - Rachel A. North
- Department
of Biochemistry and Biophysics, Stockholm
University, SE 106 91 Stockholm, Sweden
| | - Kumar Nagarathinam
- Center
of Structural and Cell Biology in Medicine, Institute of Biochemistry, University of Lübeck, D-23538, Lübeck, Germany
| | - Mikio Tanabe
- Structural
Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Oho 1-1, Tsukuba, Ibaraki 305-0801, Japan
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7
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Function Trumps Form in Two Sugar Symporters, LacY and vSGLT. Int J Mol Sci 2021; 22:ijms22073572. [PMID: 33808202 PMCID: PMC8037263 DOI: 10.3390/ijms22073572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/18/2021] [Accepted: 03/24/2021] [Indexed: 11/21/2022] Open
Abstract
Active transport of sugars into bacteria occurs through symporters driven by ion gradients. LacY is the most well-studied proton sugar symporter, whereas vSGLT is the most characterized sodium sugar symporter. These are members of the major facilitator (MFS) and the amino acid-Polyamine organocation (APS) transporter superfamilies. While there is no structural homology between these transporters, they operate by a similar mechanism. They are nano-machines driven by their respective ion electrochemical potential gradients across the membrane. LacY has 12 transmembrane helices (TMs) organized in two 6-TM bundles, each containing two 3-helix TM repeats. vSGLT has a core structure of 10 TM helices organized in two inverted repeats (TM 1–5 and TM 6–10). In each case, a single sugar is bound in a central cavity and sugar selectivity is determined by hydrogen- and hydrophobic- bonding with side chains in the binding site. In vSGLT, the sodium-binding site is formed through coordination with carbonyl- and hydroxyl-oxygens from neighboring side chains, whereas in LacY the proton (H3O+) site is thought to be a single glutamate residue (Glu325). The remaining challenge for both transporters is to determine how ion electrochemical potential gradients drive uphill sugar transport.
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8
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Li F, Egea PF, Vecchio AJ, Asial I, Gupta M, Paulino J, Bajaj R, Dickinson MS, Ferguson-Miller S, Monk BC, Stroud RM. Highlighting membrane protein structure and function: A celebration of the Protein Data Bank. J Biol Chem 2021; 296:100557. [PMID: 33744283 PMCID: PMC8102919 DOI: 10.1016/j.jbc.2021.100557] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 02/10/2021] [Accepted: 03/16/2021] [Indexed: 12/13/2022] Open
Abstract
Biological membranes define the boundaries of cells and compartmentalize the chemical and physical processes required for life. Many biological processes are carried out by proteins embedded in or associated with such membranes. Determination of membrane protein (MP) structures at atomic or near-atomic resolution plays a vital role in elucidating their structural and functional impact in biology. This endeavor has determined 1198 unique MP structures as of early 2021. The value of these structures is expanded greatly by deposition of their three-dimensional (3D) coordinates into the Protein Data Bank (PDB) after the first atomic MP structure was elucidated in 1985. Since then, free access to MP structures facilitates broader and deeper understanding of MPs, which provides crucial new insights into their biological functions. Here we highlight the structural and functional biology of representative MPs and landmarks in the evolution of new technologies, with insights into key developments influenced by the PDB in magnifying their impact.
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Affiliation(s)
- Fei Li
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA; Department of Neurology, University of California San Francisco, San Francisco, California, USA
| | - Pascal F Egea
- Department of Biological Chemistry, School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Alex J Vecchio
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | | | - Meghna Gupta
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
| | - Joana Paulino
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
| | - Ruchika Bajaj
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA
| | - Miles Sasha Dickinson
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
| | - Shelagh Ferguson-Miller
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Brian C Monk
- Sir John Walsh Research Institute and Department of Oral Sciences, University of Otago, North Dunedin, Dunedin, New Zealand
| | - Robert M Stroud
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA.
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9
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Geiger D. Plant glucose transporter structure and function. Pflugers Arch 2020; 472:1111-1128. [PMID: 32845347 PMCID: PMC8298354 DOI: 10.1007/s00424-020-02449-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 08/06/2020] [Accepted: 08/10/2020] [Indexed: 12/01/2022]
Abstract
The carbohydrate D-glucose is the main source of energy in living organisms. In contrast to animals, as well as most fungi, bacteria, and archaea, plants are capable to synthesize a surplus of sugars characterizing them as autothrophic organisms. Thus, plants are de facto the source of all food on earth, either directly or indirectly via feed to livestock. Glucose is stored as polymeric glucan, in animals as glycogen and in plants as starch. Despite serving a general source for metabolic energy and energy storage, glucose is the main building block for cellulose synthesis and represents the metabolic starting point of carboxylate- and amino acid synthesis. Finally yet importantly, glucose functions as signalling molecule conveying the plant metabolic status for adjustment of growth, development, and survival. Therefore, cell-to-cell and long-distance transport of photoassimilates/sugars throughout the plant body require the fine-tuned activity of sugar transporters facilitating the transport across membranes. The functional plant counterparts of the animal sodium/glucose transporters (SGLTs) are represented by the proton-coupled sugar transport proteins (STPs) of the plant monosaccharide transporter(-like) family (MST). In the framework of this special issue on “Glucose Transporters in Health and Disease,” this review gives an overview of the function and structure of plant STPs in comparison to the respective knowledge obtained with the animal Na+-coupled glucose transporters (SGLTs).
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Affiliation(s)
- Dietmar Geiger
- Institute for Molecular Plant Physiology and Biophysics, Julius-von-Sachs-Institute, Biocenter, University of Wuerzburg, 97082, Wuerzburg, Germany.
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10
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Omeis F, Santos Seica AF, Ermolova N, Kaback HR, Hellwig P. Monoclonal antibody 4B1 influences the pK a of Glu325 in lactose permease (LacY) from Escherichia coli: evidence from SEIRAS. FEBS Lett 2020; 594:3356-3362. [PMID: 32780424 DOI: 10.1002/1873-3468.13907] [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: 06/19/2020] [Revised: 08/05/2020] [Accepted: 08/06/2020] [Indexed: 11/11/2022]
Abstract
The monoclonal antibody 4B1 binds to a conformational epitope on the periplasmic side of lactose permease (LacY) of Escherichia coli and inhibits H+ /lactose symport and lactose efflux under nonenergized conditions. At the same time, ligand binding and translocation reactions that do not involve net H+ translocation remain unaffected by 4B1. In this study, surface-enhanced infrared absorption spectroscopy applied to the immobilized LacY was used to study the pH-dependent changes in LacY and to access in situ the effect of the 4B1 antibody on the pKa of Glu325, the primary functional H+ -binding site in LacY. A small shift of the pK value from 10.5 to 9.5 was identified that can be corroborated with the inactivation of LacY upon 4B1 binding.
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Affiliation(s)
- Fatima Omeis
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, CMC, Université de Strasbourg CNRS, Strasbourg, France.,University of Strasbourg Institute for Advanced Studies (USIAS), Strasbourg, France
| | - Ana Filipa Santos Seica
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, CMC, Université de Strasbourg CNRS, Strasbourg, France
| | - Natalia Ermolova
- Department of Physiology, University of California, Los Angeles, CA, USA
| | - H Ronald Kaback
- Department of Physiology, University of California, Los Angeles, CA, USA.,Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, CA, USA.,Molecular Biology Institute, University of California, Los Angeles, CA, USA
| | - Petra Hellwig
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, CMC, Université de Strasbourg CNRS, Strasbourg, France.,University of Strasbourg Institute for Advanced Studies (USIAS), Strasbourg, France
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11
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Diversity in kinetics correlated with structure in nano body-stabilized LacY. PLoS One 2020; 15:e0232846. [PMID: 32380514 PMCID: PMC7205474 DOI: 10.1371/journal.pone.0232846] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 04/22/2020] [Indexed: 12/04/2022] Open
Abstract
The structure of lactose permease, stabilized in a periplasmic open conformation by two Gly to Trp replacements (LacYww) and complexed with a nanobody directed against this conformation, provides the highest resolution structure of the symporter. The nanobody binds in a different manner than two other nanobodies made against the same mutant, which also bind to the same general region on the periplasmic side. This region of the protein may represent an immune hotspot. The CDR3 loop of the nanobody is held by hydrogen bonds in a conformation that partially blocks access to the substrate-binding site. As a result, kon and koff for galactoside binding to either LacY or the double mutant complexed with the nanobody are lower than for the other two LacY/nanobody complexes though the Kd values are similar, reflecting the fact that the nanobodies rigidify structures along the pathway. While the wild-type LacY/nanobody complex clearly stabilizes a similar ‘extracellular open’ conformation in solution, judged by binding kinetics, the complex with wild-type LacY did not yet crystallize, suggesting the nanobody does not bind strongly enough to shift the equilibrium to stabilize a periplasmic side-open conformation suitable for crystallization. However, the similarity of the galactoside binding kinetics for the nanobody-bound complexes with wild type LacY and with LacYWW indicates that they have similar structures, showing that the reported co-structures reliably show nanobody interactions with LacY.
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12
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Wiriyasermkul P, Moriyama S, Nagamori S. Membrane transport proteins in melanosomes: Regulation of ions for pigmentation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183318. [PMID: 32333855 PMCID: PMC7175901 DOI: 10.1016/j.bbamem.2020.183318] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/17/2020] [Accepted: 04/18/2020] [Indexed: 12/12/2022]
Abstract
Melanosomes are unique organelles in melanocytes that produce melanin, the pigment for skin, hair, and eye color. Tyrosinase is the essential and rate-limiting enzyme for melanin production, that strictly requires neutral pH for activity. pH maintenance is a result of the combinational function of multiple ion transport proteins. Thus, ion homeostasis in melanosomes is crucial for melanin synthesis. Defect of the ion transport system causes various pigmentation phenotypes, from mild effect to severe disorders such as albinism. In this review, we summarize the up-to-date knowledge of the ion transport system, such as transport function, structure, and the physiological roles and mechanisms of the ion transport proteins in melanosomes. In addition, we propose a model of melanosomal ion transport system-how the functional coupling of multiple transport proteins modulates and maintains ion homeostasis. We discuss melanin synthesis in terms of the ion transport system.
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Affiliation(s)
- Pattama Wiriyasermkul
- Department of Collaborative Research for Bio-Molecular Dynamics, Nara Medical University, 840 Shijo-cho, Kashihara, Nara 634-8521, Japan
| | - Satomi Moriyama
- Department of Collaborative Research for Bio-Molecular Dynamics, Nara Medical University, 840 Shijo-cho, Kashihara, Nara 634-8521, Japan
| | - Shushi Nagamori
- Department of Collaborative Research for Bio-Molecular Dynamics, Nara Medical University, 840 Shijo-cho, Kashihara, Nara 634-8521, Japan.
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13
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14
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Uchański T, Pardon E, Steyaert J. Nanobodies to study protein conformational states. Curr Opin Struct Biol 2020; 60:117-123. [DOI: 10.1016/j.sbi.2020.01.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/08/2020] [Accepted: 01/09/2020] [Indexed: 01/07/2023]
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15
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Kumar S, Mahendran I, Athreya A, Ranjan R, Penmatsa A. Isolation and structural characterization of a Zn 2+-bound single-domain antibody against NorC, a putative multidrug efflux transporter in bacteria. J Biol Chem 2020; 295:55-68. [PMID: 31699895 PMCID: PMC6952597 DOI: 10.1074/jbc.ra119.010902] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 11/06/2019] [Indexed: 12/15/2022] Open
Abstract
Single-chain antibodies from camelids have served as powerful tools ranging from diagnostics and therapeutics to crystallization chaperones meant to study protein structure and function. In this study, we isolated a single-chain antibody from an Indian dromedary camel (ICab) immunized against a bacterial 14TM helix transporter, NorC, from Staphylococcus aureus We identified this antibody in a yeast display screen built from mononuclear cells isolated from the immunized camel and purified the antibody from Escherichia coli after refolding it from inclusion bodies. The X-ray structure of the antibody at 2.15 Å resolution revealed a unique feature within its CDR3 loop, which harbors a Zn2+-binding site that substitutes for a loop-stabilizing disulfide bond. We performed mutagenesis to compromise the Zn2+-binding site and observed that this change severely hampered antibody stability and its ability to interact with the antigen. The lack of bound Zn2+ also made the CDR3 loop highly flexible, as observed in all-atom simulations. Using confocal imaging of NorC-expressing E. coli spheroplasts, we found that the ICab interacts with the extracellular surface of NorC. This suggests that the ICab could be a valuable tool for detecting methicillin-resistant S. aureus strains that express efflux transporters such as NorC in hospital and community settings.
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Affiliation(s)
- Sushant Kumar
- Molecular Biophysics Unit, Indian Institute of Science, CV Raman Road, Bengaluru 560012, India
| | - Ithayaraja Mahendran
- Molecular Biophysics Unit, Indian Institute of Science, CV Raman Road, Bengaluru 560012, India
| | - Arunabh Athreya
- Molecular Biophysics Unit, Indian Institute of Science, CV Raman Road, Bengaluru 560012, India
| | - Rakesh Ranjan
- National Research Centre on Camel, Jorbeer, Bikaner, Rajasthan 334001, India
| | - Aravind Penmatsa
- Molecular Biophysics Unit, Indian Institute of Science, CV Raman Road, Bengaluru 560012, India.
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16
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The proton electrochemical gradient induces a kinetic asymmetry in the symport cycle of LacY. Proc Natl Acad Sci U S A 2019; 117:977-981. [PMID: 31889006 PMCID: PMC6969543 DOI: 10.1073/pnas.1916563117] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Protonation and deprotonation of Glu325 with a pKa of 10.5 is required for symport. Moreover, the H+ electrochemical gradient (∆μ∼H+) accelerates deprotonation on the intracellular side with a 50- to 100-fold decrease in the Km. To probe the pK on the cytoplasmic side of the membrane, rates of lactose/H+ efflux were determined from pH 5.0 to 9.0 without or with a membrane potential (ΔΨ, interior positive) in right-side-out membrane vesicles. WT lactose efflux has an apparent pK of ∼7.2 that is unaffected by ΔΨ, mutant E325A is defective, and pH or ΔΨ (interior positive) has no effect. The effect of ΔΨ (interior positive) on the Km for efflux with WT LacY is insignificant relative to the marked effect on influx. LacY catalyzes accumulation of galactosides against a concentration gradient by coupling galactoside and H+ transport (i.e., symport). While alternating access of sugar- and H+-binding sites to either side of the membrane is driven by binding and dissociation of sugar, the electrochemical H+ gradient (∆μ∼H+) functions kinetically by decreasing the Km for influx 50- to 100-fold with no change in Kd. The affinity of protonated LacY for sugar has an apparent pK (pKapp) of ∼10.5, due specifically to the pKa of Glu325, a residue that plays an irreplaceable role in coupling. In this study, rates of lactose/H+ efflux were measured from pH 5.0 to 9.0 in the absence or presence of a membrane potential (ΔΨ, interior positive), and the effect of the imposed ΔΨ on the kinetics of efflux was also studied in right-side-out membrane vesicles. The findings reveal that ∆μ∼H+ induces an asymmetry in the transport cycle based on the following observations: 1) the efflux rate of WT LacY exhibits a pKapp of ∼7.2 that is unaffected by the imposed ΔΨ; 2) ΔΨ increases the rate of efflux at all tested pH values, but enhancement is almost 2 orders of magnitude less than observed for influx; 3) mutant Glu325 ˗ Ala does little or no efflux in the absence or presence of ΔΨ, and ambient pH has no effect; and 4) the effect of ΔΨ (interior positive) on the Km for efflux is almost insignificant relative to the 50- to 100-fold decrease in the Km for influx driven by ΔΨ (interior negative).
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17
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Kaback HR, Guan L. It takes two to tango: The dance of the permease. J Gen Physiol 2019; 151:878-886. [PMID: 31147449 PMCID: PMC6605686 DOI: 10.1085/jgp.201912377] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 05/14/2019] [Indexed: 11/20/2022] Open
Abstract
The lactose permease (LacY) of Escherichia coli is the prototype of the major facilitator superfamily, one of the largest families of membrane transport proteins. Structurally, two pseudo-symmetrical six-helix bundles surround a large internal aqueous cavity. Single binding sites for galactoside and H+ are positioned at the approximate center of LacY halfway through the membrane at the apex of the internal cavity. These features enable LacY to function by an alternating-access mechanism that can catalyze galactoside/H+ symport in either direction across the cytoplasmic membrane. The H+-binding site is fully protonated under physiological conditions, and subsequent sugar binding causes transition of the ternary complex to an occluded intermediate that can open to either side of the membrane. We review the structural and functional evidence that has provided new insight into the mechanism by which LacY achieves active transport against a concentration gradient.
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Affiliation(s)
- H Ronald Kaback
- Department of Physiology and Department of Microbiology, Immunology and Molecular Genetics, Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Center of Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX
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18
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Abstract
Carrasco reflects on her postdoctoral advisor, Ron Kaback—an exceptional scientist and inspiring mentor.
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Affiliation(s)
- Nancy Carrasco
- Department of Cellular & Molecular Physiology, Yale School of Medicine, New Haven, CT
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19
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Abstract
Transport of solutes across biological membranes is essential for cellular life. This process is mediated by membrane transport proteins which move nutrients, waste products, certain drugs and ions into and out of cells. Secondary active transporters couple the transport of substrates against their concentration gradients with the transport of other solutes down their concentration gradients. The alternating access model of membrane transporters and the coupling mechanism of secondary active transporters are introduced in this book chapter. Structural studies have identified typical protein folds for transporters that we exemplify by the major facilitator superfamily (MFS) and LeuT folds. Finally, substrate binding and substrate translocation of the transporters LacY of the MFS and AdiC of the amino acid-polyamine-organocation (APC) superfamily are described.
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Affiliation(s)
- Patrick D Bosshart
- Swiss National Centre of Competence in Research (NCCR) TransCure, Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012, Bern, Switzerland
| | - Dimitrios Fotiadis
- Swiss National Centre of Competence in Research (NCCR) TransCure, Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012, Bern, Switzerland.
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20
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Abstract
The lactose permease of Escherichia coli (LacY) utilizes an alternating access symport mechanism with multiple conformational intermediates, but only inward (cytoplasmic)- or outward (periplasmic)-open structures have been characterized by X-ray crystallography. It is demonstrated here with sugar-binding studies that cross-linking paired-Cys replacements across the closed cytoplasmic cavity stabilize an occluded conformer with an inaccessible sugar-binding site. In addition, a nanobody (Nb) that stabilizes a periplasmic-open conformer with an easily accessible sugar-binding site in WT LacY fails to cause the cytoplasmic cross-linked mutants to become accessible to galactoside, showing that the periplasmic cavity is closed. These results are consistent with tight association of the periplasmic ends in two pairs of helices containing clusters of small residues in the packing interface between N- and C-terminal six-helix bundles of the symporter. However, after reduction of the disulfide bond, the Nb markedly increases the rate of galactoside binding, indicating unrestricted access to the Nb epitope and the galactoside-binding site from the periplasm. The findings indicate that the cross-linked cytoplasmic double-Cys mutants resemble an occluded apo-intermediate in the transport cycle.
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21
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Vishwakarma P, Banerjee A, Pasrija R, Prasad R, Lynn AM. Phylogenetic and conservation analyses of MFS transporters. 3 Biotech 2018; 8:462. [PMID: 30370203 DOI: 10.1007/s13205-018-1476-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 10/11/2018] [Indexed: 12/21/2022] Open
Abstract
Major facilitator superfamily is one of the largest superfamily of secondary transporters present across the kingdom of life. Considering the physiological and clinical importance of MFS proteins, we attempted to explore the phylogenetic and structural aspects of the superfamily. To achieve the objectives, we performed global sequence-based analyses of MFS proteins encompassing multiple taxa. Notably, phylogenetic analysis of MFS proteins resulted in the clustering of MFS proteins based on their function, rather than lineage of the respective organisms. Additionally, we employed information theoretic measures, Relative entropy (RE) and Cumulative relative entropy (CRE) to decipher fold-specific and function-specific residues, respectively, in the MFS proteins. The residues with high RE score when mapped on to the 3D-structure of MFS transporter LacY, were found to be distributed throughout the tertiary structure of the protein. On the other hand, CRE calculation was employed to contrast two subfamilies Drug H+ antiporter 1 and 3 (DHA1 and DHA3). The particular analysis unveiled certain differentially conserved residues in DHA1 as compared to DHA3 highlighting family-specific importance of them. Remarkably, a number of high scoring CRE residues have already established functional roles, for instance, the arginine residue present in TMH4. Altogether, the current study apart from providing an insight into the functional clustering of MFS proteins also identifies residues with established or plausible roles in the transport mechanism. Thus, the study lays a platform for future structure-function studies of these proteins.
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Affiliation(s)
- Poonam Vishwakarma
- 1School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
- 2Department of Biochemistry, Maharshi Dayanand University, Rohtak, Haryana India
| | - Atanu Banerjee
- 1School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Ritu Pasrija
- 2Department of Biochemistry, Maharshi Dayanand University, Rohtak, Haryana India
| | - Rajendra Prasad
- 3Amity Institute of Integrative Sciences and Health, Amity Institute of Biotechnology, Amity University Haryana, Gurgaon, India
| | - Andrew M Lynn
- 1School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
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22
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Nagarathinam K, Nakada-Nakura Y, Parthier C, Terada T, Juge N, Jaenecke F, Liu K, Hotta Y, Miyaji T, Omote H, Iwata S, Nomura N, Stubbs MT, Tanabe M. Outward open conformation of a Major Facilitator Superfamily multidrug/H + antiporter provides insights into switching mechanism. Nat Commun 2018; 9:4005. [PMID: 30275448 PMCID: PMC6167325 DOI: 10.1038/s41467-018-06306-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 08/13/2018] [Indexed: 12/14/2022] Open
Abstract
Multidrug resistance (MDR) poses a major challenge to medicine. A principle cause of MDR is through active efflux by MDR transporters situated in the bacterial membrane. Here we present the crystal structure of the major facilitator superfamily (MFS) drug/H+ antiporter MdfA from Escherichia coli in an outward open conformation. Comparison with the inward facing (drug binding) state shows that, in addition to the expected change in relative orientations of the N- and C-terminal lobes of the antiporter, the conformation of TM5 is kinked and twisted. In vitro reconstitution experiments demonstrate the importance of selected residues for transport and molecular dynamics simulations are used to gain insights into antiporter switching. With the availability of structures of alternative conformational states, we anticipate that MdfA will serve as a model system for understanding drug efflux in MFS MDR antiporters. The multidrug resistance transporter mediated efflux of antibiotics from the bacterial cytoplasm represents a major challenge to medicine. Here authors solve the X-ray crystallographic structure of the drug/H+ antiporter MdfA from Escherichia coli and shed light on the conformational switching mechanism.
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Affiliation(s)
- Kumar Nagarathinam
- ZIK HALOmem, Kurt-Mothes-Straße 3, D-06120, Halle/Saale, Germany.,Institut für Biochemie und Biotechnologie, Charles-Tanford-Proteinzentrum, Martin-Luther Universität Halle-Wittenberg, Kurt-Mothes-Straße 3a, D-06120, Halle/Saale, Germany.,Institute of Virology, Hannover Medical School, Carl-Neuberg-Straße 1, D-30625, Hannover, Germany
| | - Yoshiko Nakada-Nakura
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Christoph Parthier
- Institut für Biochemie und Biotechnologie, Charles-Tanford-Proteinzentrum, Martin-Luther Universität Halle-Wittenberg, Kurt-Mothes-Straße 3a, D-06120, Halle/Saale, Germany
| | - Tohru Terada
- Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Narinobu Juge
- Advanced Science Research Center, Okayama University, 1-1-1 Kita-ku, Tsushima-naka, Okayama, 700-8530, Japan
| | - Frank Jaenecke
- ZIK HALOmem, Kurt-Mothes-Straße 3, D-06120, Halle/Saale, Germany
| | - Kehong Liu
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Yunhon Hotta
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Takaaki Miyaji
- Advanced Science Research Center, Okayama University, 1-1-1 Kita-ku, Tsushima-naka, Okayama, 700-8530, Japan
| | - Hiroshi Omote
- Department of Membrane Biochemistry, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 1-1-1 Kita-ku, Tsushima-naka, Okayama, 700-8530, Japan
| | - So Iwata
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, 606-8501, Japan.,RIKEN, SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
| | - Norimichi Nomura
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Milton T Stubbs
- ZIK HALOmem, Kurt-Mothes-Straße 3, D-06120, Halle/Saale, Germany. .,Institut für Biochemie und Biotechnologie, Charles-Tanford-Proteinzentrum, Martin-Luther Universität Halle-Wittenberg, Kurt-Mothes-Straße 3a, D-06120, Halle/Saale, Germany.
| | - Mikio Tanabe
- ZIK HALOmem, Kurt-Mothes-Straße 3, D-06120, Halle/Saale, Germany. .,Structural Biology Research Center, Institute of Materials Structure Science, KEK/High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan.
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23
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Uptake dynamics in the Lactose permease (LacY) membrane protein transporter. Sci Rep 2018; 8:14324. [PMID: 30254312 PMCID: PMC6156506 DOI: 10.1038/s41598-018-32624-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 09/12/2018] [Indexed: 11/08/2022] Open
Abstract
The sugar transporter Lactose permease (LacY) of Escherichia coli has become a prototype to understand the underlying molecular details of membrane transport. Crystal structures have trapped the protein in sugar-bound states facing the periplasm, but with narrow openings unable to accommodate sugar. Therefore, the molecular details of sugar uptake remain elusive. In this work, we have used extended simulations and metadynamics sampling to explore a putative sugar-uptake pathway and associated free energy landscape. We found an entrance at helix-pair 2 and 11, which involved lipid head groups and residues Gln 241 and Gln 359. Furthermore, the protein displayed high flexibility on the periplasmic side of Phe 27, which is located at the narrowest section of the pathway. Interactions to Phe 27 enabled passage into the binding site, which was associated with a 24 ± 4 kJ/mol binding free energy in excellent agreement with an independent binding free energy calculation and experimental data. Two free energy minima corresponding to the two possible binding poses of the lactose analog β-D-galactopyranosyl-1-thio-β-D-galactopyranoside (TDG) were aligned with the crystal structure-binding pocket. This work outlines the chemical environment of a putative periplasmic sugar pathway and paves way for understanding substrate affinity and specificity in LacY.
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24
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Abstract
The lactose permease of Escherichia coli (LacY), a dynamic polytopic membrane transport protein, catalyzes galactoside/H+ symport and operates by an alternating access mechanism that exhibits multiple conformations, the distribution of which is altered by sugar-binding. Camelid nanobodies were made against a double-mutant Gly46 → Trp/Gly262 → Trp (LacYWW) that produces an outward-open conformation, as opposed to the cytoplasmic open-state crystal structure of WT LacY. Nanobody 9047 (Nb9047) stabilizes WT LacY in a periplasmic-open conformation. Here, we describe the X-ray crystal structure of a complex between LacYWW, the high-affinity substrate analog 4-nitrophenyl-α-d-galactoside (NPG), and Nb9047 at 3-Å resolution. The present crystal structure demonstrates that Nb9047 binds to the periplasmic face of LacY, primarily to the C-terminal six-helical bundle, while a flexible loop of the Nb forms a bridge between the N- and C-terminal halves of LacY across the periplasmic vestibule. The bound Nb partially covers the vestibule, yet does not affect the on-rates or off-rates for the substrate binding to LacYWW, which implicates dynamic flexibility of the Nb-LacYWW complex. Nb9047-binding neither changes the overall structure of LacYWW with bound NPG, nor the positions of side chains comprising the galactoside-binding site. The current NPG-bound structure exhibits a more occluded periplasmic vestibule than seen in a previous structure of a (different Nb) apo-LacYWW/Nb9039 complex that we argue is caused by sugar-binding, with major differences located at the periplasmic ends of transmembrane helices in the N-terminal half of LacY.
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25
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Yaffe D, Forrest LR, Schuldiner S. The ins and outs of vesicular monoamine transporters. J Gen Physiol 2018; 150:671-682. [PMID: 29666153 PMCID: PMC5940252 DOI: 10.1085/jgp.201711980] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 03/26/2018] [Indexed: 01/31/2023] Open
Abstract
Yaffe et al. review structure-guided studies that have provided insight into the mechanism of proton-monoamine antiport by VMATs. The H+-coupled vesicular monoamine transporter (VMAT) is a transporter essential for life. VMAT mediates packaging of the monoamines serotonin, dopamine, norepinephrine, and histamine from the neuronal cytoplasm into presynaptic vesicles, which is a key step in the regulated release of neurotransmitters. However, a detailed understanding of the mechanism of VMAT function has been limited by the lack of availability of high-resolution structural data. In recent years, a series of studies guided by homology models has revealed significant insights into VMAT function, identifying residues that contribute to the binding site and to specific steps in the transport cycle. Moreover, to characterize the conformational transitions that occur upon binding of the substrate and coupling ion, we have taken advantage of the unique and powerful pharmacology of VMAT as well as of mutants that affect the conformational equilibrium of the protein and shift it toward defined conformations. This has allowed us to identify an important role for the proton gradient in driving a shift from lumen-facing to cytoplasm-facing conformations.
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Affiliation(s)
- Dana Yaffe
- Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, Hebrew University, Jerusalem, Israel
| | - Lucy R Forrest
- Computational Structural Biology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
| | - Shimon Schuldiner
- Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, Hebrew University, Jerusalem, Israel
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26
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Bai X, Moraes TF, Reithmeier RAF. Structural biology of solute carrier (SLC) membrane transport proteins. Mol Membr Biol 2018; 34:1-32. [PMID: 29651895 DOI: 10.1080/09687688.2018.1448123] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The human solute carriers (SLCs) comprise over 400 different transporters, organized into 65 families ( http://slc.bioparadigms.org/ ) based on their sequence homology and transport function. SLCs are responsible for transporting extraordinarily diverse solutes across biological membranes, including inorganic ions, amino acids, lipids, sugars, neurotransmitters and drugs. Most of these membrane proteins function as coupled symporters (co-transporters) utilizing downhill ion (H+ or Na+) gradients as the driving force for the transport of substrate against its concentration gradient into cells. Other members work as antiporters (exchangers) that typically contain a single substrate-binding site with an alternating access mode of transport, while a few members exhibit channel-like properties. Dysfunction of SLCs is correlated with numerous human diseases and therefore they are potential therapeutic drug targets. In this review, we identified all of the SLC crystal structures that have been determined, most of which are from prokaryotic species. We further sorted all the SLC structures into four main groups with different protein folds and further discuss the well-characterized MFS (major facilitator superfamily) and LeuT (leucine transporter) folds. This review provides a systematic analysis of the structure, molecular basis of substrate recognition and mechanism of action in different SLC family members.
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Affiliation(s)
- Xiaoyun Bai
- a Department of Biochemistry , University of Toronto , Toronto , Canada
| | - Trevor F Moraes
- a Department of Biochemistry , University of Toronto , Toronto , Canada
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27
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Köhler M, Neff C, Perez C, Brunner C, Pardon E, Steyaert J, Schneider G, Locher KP, Zenobi R. Binding Specificities of Nanobody•Membrane Protein Complexes Obtained from Chemical Cross-Linking and High-Mass MALDI Mass Spectrometry. Anal Chem 2018; 90:5306-5313. [PMID: 29562137 DOI: 10.1021/acs.analchem.8b00236] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The application of nanobodies as binding partners for structure stabilization in protein X-ray crystallography is taking an increasingly important role in structural biology. However, the addition of nanobodies to the crystallization matrices might complicate the optimization of the crystallization process, which is why analytical techniques to screen and characterize suitable nanobodies are useful. Here, we show how chemical cross-linking combined with high-mass matrix-assisted laser/desorption ionization mass spectrometry can be employed as a fast screening technique to determine binding specificities of intact nanobody•membrane protein complexes. Titration series were performed to rank the binding affinity of the interacting nanobodies. To validate the mass spectrometry data, microscale thermophoresis was used, which showed binding affinities of the stronger binding nanobodies, in the low μM range. In addition, mass spectrometry provides access to the stoichiometry of the complexes formed, which enables the definition of conditions under which homogeneous complex states are present in solution. Conformational changes of the membrane protein were investigated and competitive binding experiments were used to delimit the interaction sites of the nanobodies, which is in agreement with crystal structures obtained. The results show the diversity of specifically binding nanobodies in terms of binding affinity, stoichiometry, and binding site, which illustrates the need for an analytical screening approach.
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Affiliation(s)
- Martin Köhler
- Department of Chemistry and Applied Biosciences , ETH Zürich , Vladimir-Prelog-Weg 3 , 8093 Zurich , Switzerland
| | - Christoph Neff
- Department of Chemistry and Applied Biosciences , ETH Zürich , Vladimir-Prelog-Weg 3 , 8093 Zurich , Switzerland
| | - Camilo Perez
- Institute of Molecular Biology and Biophysics , ETH Zürich , Otto-Stern-Weg 5 , 8093 Zurich , Switzerland
| | - Cyrill Brunner
- Department of Chemistry and Applied Biosciences , ETH Zürich , Vladimir-Prelog-Weg 3 , 8093 Zurich , Switzerland
| | | | | | - Gisbert Schneider
- Department of Chemistry and Applied Biosciences , ETH Zürich , Vladimir-Prelog-Weg 3 , 8093 Zurich , Switzerland
| | - Kaspar P Locher
- Institute of Molecular Biology and Biophysics , ETH Zürich , Otto-Stern-Weg 5 , 8093 Zurich , Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences , ETH Zürich , Vladimir-Prelog-Weg 3 , 8093 Zurich , Switzerland
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28
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Oversized galactosides as a probe for conformational dynamics in LacY. Proc Natl Acad Sci U S A 2018; 115:4146-4151. [PMID: 29602806 DOI: 10.1073/pnas.1800706115] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Binding kinetics of α-galactopyranoside homologs with fluorescent aglycones of different sizes and shapes were determined with the lactose permease (LacY) of Escherichia coli by FRET from Trp151 in the binding site of LacY to the fluorophores. Fast binding was observed with LacY stabilized in an outward-open conformation (kon = 4-20 μM-1·s-1), indicating unobstructed access to the binding site even for ligands that are much larger than lactose. Dissociation rate constants (koff) increase with the size of the aglycone so that Kd values also increase but remain in the micromolar range for each homolog. Phe27 (helix I) forms an apparent constriction in the pathway for sugar by protruding into the periplasmic cavity. However, replacement of Phe27 with a bulkier Trp does not create an obstacle in the pathway even for large ligands, since binding kinetics remain unchanged. High accessibility of the binding site is also observed in a LacY/nanobody complex with partially blocked periplasmic opening. Remarkably, E. coli expressing WT LacY catalyzes transport of α- or β-galactopyranosides with oversized aglycones such as bodipy or Aldol518, which may require an extra space within the occluded intermediate. The results confirm that LacY specificity is strictly directed toward the galactopyranoside ring and also clearly indicate that the opening on the periplasmic side is sufficiently wide to accommodate the large galactoside derivatives tested here. We conclude that the actual pathway for the substrate entering from the periplasmic side is wider than the pore diameter calculated in the periplasmic-open X-ray structures.
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29
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Schubert AF, Gladkova C, Pardon E, Wagstaff JL, Freund SM, Steyaert J, Maslen SL, Komander D. Structure of PINK1 in complex with its substrate ubiquitin. Nature 2017; 552:51-56. [PMID: 29160309 PMCID: PMC6020998 DOI: 10.1038/nature24645] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 10/20/2017] [Indexed: 12/28/2022]
Abstract
Autosomal-recessive juvenile Parkinsonism (AR-JP) is caused by mutations in a number of PARK genes, in particular the genes encoding the E3 ubiquitin ligase Parkin (PARK2, also known as PRKN) and its upstream protein kinase PINK1 (also known as PARK6). PINK1 phosphorylates both ubiquitin and the ubiquitin-like domain of Parkin on structurally protected Ser65 residues, triggering mitophagy. Here we report a crystal structure of a nanobody-stabilized complex containing Pediculus humanus corporis (Ph)PINK1 bound to ubiquitin in the 'C-terminally retracted' (Ub-CR) conformation. The structure reveals many peculiarities of PINK1, including the architecture of the C-terminal region, and reveals how the N lobe of PINK1 binds ubiquitin via a unique insertion. The flexible Ser65 loop in the Ub-CR conformation contacts the activation segment, facilitating placement of Ser65 in a phosphate-accepting position. The structure also explains how autophosphorylation in the N lobe stabilizes structurally and functionally important insertions, and reveals the molecular basis of AR-JP-causing mutations, some of which disrupt ubiquitin binding.
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Affiliation(s)
- Alexander F. Schubert
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Christina Gladkova
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Els Pardon
- VIB-VUB Center for Structural Biology, VIB, 1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Jane L. Wagstaff
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Stefan M.V. Freund
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Jan Steyaert
- VIB-VUB Center for Structural Biology, VIB, 1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Sarah L. Maslen
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - David Komander
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
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30
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The folding, stability and function of lactose permease differ in their dependence on bilayer lipid composition. Sci Rep 2017; 7:13056. [PMID: 29026149 PMCID: PMC5638818 DOI: 10.1038/s41598-017-13290-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 09/19/2017] [Indexed: 11/22/2022] Open
Abstract
Lipids play key roles in Biology. Mechanical properties of the lipid bilayer influence their neighbouring membrane proteins, however it is unknown whether different membrane protein properties have the same dependence on membrane mechanics, or whether mechanics are tuned to specific protein processes of the protein. We study the influence of lipid lateral pressure and electrostatic effects on the in vitro reconstitution, folding, stability and function of a representative of the ubiquitous major facilitator transporter superfamily, lactose permease. Increasing the outward chain lateral pressure in the bilayer, through addition of lamellar phosphatidylethanolamine lipids, lowers lactose permease folding and reconstitution yields but stabilises the folded state. The presence of phosphatidylethanolamine is however required for correct folding and function. An increase in headgroup negative charge through the addition of phosphatidylglycerol lipids favours protein reconstitution but is detrimental to topology and function. Overall the in vitro folding, reconstitution, topology, stability and function of lactose permease are found to have different dependences on bilayer composition. A regime of lipid composition is found where all properties are favoured, even if suboptimal. This lays ground rules for rational control of membrane proteins in nanotechnology and synthetic biology by manipulating global bilayer properties to tune membrane protein behaviour.
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Jewel Y, Dutta P, Liu J. Exploration of conformational changes in lactose permease upon sugar binding and proton transfer through coarse-grained simulations. Proteins 2017. [PMID: 28639287 DOI: 10.1002/prot.25340] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Escherichia coli lactose permease (LacY) actively transports lactose and other galactosides across cell membranes through lactose/H+ symport process. Lactose/H+ symport is a highly complex process that involves sugar translocation, H+ transfer, and large-scale protein conformational changes. The complete picture of lactose/H+ symport is largely unclear due to the complexity and multiscale nature of the process. In this work, we develop the force field for sugar molecules compatible with PACE, a hybrid and coarse-grained force field that couples the united-atom protein models with the coarse-grained MARTINI water/lipid. After validation, we implement the new force field to investigate the binding of a β-d-galactopyranosyl-1-thio- β-d-galactopyranoside (TDG) molecule to a wild-type LacY. Results show that the local interactions between TDG and LacY at the binding pocket are consistent with the X-ray experiment. Transitions from inward-facing to outward-facing conformations upon TDG binding and protonation of Glu269 have been achieved from ∼5.5 µs simulations. Both the opening of the periplasmic side and closure of the cytoplasmic side of LacY are consistent with double electron-electron resonance and thiol cross-linking experiments. Our analysis suggests that the conformational changes of LacY are a cumulative consequence of interdomain H-bonds breaking at the periplasmic side, interdomain salt-bridge formation at the cytoplasmic side, and the TDG orientational changes during the transition.
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Affiliation(s)
- Yead Jewel
- School of Mechanical and Materials Engineering, Washington State University, Pullman, Washington, 99164
| | - Prashanta Dutta
- School of Mechanical and Materials Engineering, Washington State University, Pullman, Washington, 99164
| | - Jin Liu
- School of Mechanical and Materials Engineering, Washington State University, Pullman, Washington, 99164
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Structural basis of inhibition of lipid-linked oligosaccharide flippase PglK by a conformational nanobody. Sci Rep 2017; 7:46641. [PMID: 28422165 PMCID: PMC5395944 DOI: 10.1038/srep46641] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 03/21/2017] [Indexed: 12/16/2022] Open
Abstract
PglK is an ABC transporter that flips a lipid-linked oligosaccharide (LLO) that serves as a donor in protein N-glycosylation. Previous structures revealed two inward-facing conformations, both with very large separations of the nucleotide binding domains (NBDs), and a closed, ADP-bound state that featured an occluded cavity. To investigate additional states, we developed conformation-sensitive, single-domain camelid nanobodies (Nb) and studied their effect on PglK activity. Biochemical, structural, and mass spectrometric analyses revealed that one inhibitory Nb binds as a single copy to homodimeric PglK. The co-crystal structure of this Nb and ADP-bound PglK revealed a new, narrowly inward-open conformation. Rather than inducing asymmetry in the PglK homodimer, the binding of one Nb results in steric constraints that prevent a second Nb to access the symmetry-related site in PglK. The Nb performed its inhibitory role by a “sticky-doorstop” mechanism, where inhibition of ATP hydrolysis and LLO flipping activity occurs due to impaired closing of the NBD interface, which prevents PglK from converting to an outward-open conformation. This inhibitory mode suggests tight conformational coupling between the ATPase sites, which may apply to other ABC transporters.
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Abstract
Galactoside/H+ symport by the lactose permease of Escherichia coli (LacY) involves reciprocal opening and closing of periplasmic and cytoplasmic cavities so that sugar- and H+-binding sites become alternatively accessible to either side of the membrane. After reconstitution into proteoliposomes, LacY with the periplasmic cavity sealed by cross-linking paired-Cys residues does not bind sugar from the periplasmic side. However, reduction of the S-S bond restores opening of the periplasmic cavity and galactoside binding. Furthermore, nanobodies that stabilize the double-Cys mutant in a periplasmic-open conformation and allow free access of galactoside to the binding site do so only after reduction of the S-S bond. In contrast, when cross-linked LacY is solubilized in detergent, galactoside binding is observed, indicating that the cytoplasmic cavity is patent. Sugar binding from the cytoplasmic side exhibits nonlinear stopped-flow kinetics, and analysis reveals a two-step process in which a conformational change precedes binding. Because the cytoplasmic cavity is spontaneously closing and opening in the symporter with a sealed periplasmic cavity, it is apparent that an asymmetrical conformational transition controls access of sugar to the binding site.
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Affiliation(s)
- Irina Smirnova
- Department of Physiology, University of California Los Angeles, Los Angeles, California 90095-7327, United States
| | - Vladimir Kasho
- Department of Physiology, University of California Los Angeles, Los Angeles, California 90095-7327, United States
| | - Xiaoxu Jiang
- Department of Physiology, University of California Los Angeles, Los Angeles, California 90095-7327, United States
| | - H. Ronald Kaback
- Department of Physiology, University of California Los Angeles, Los Angeles, California 90095-7327, United States
- Department of Microbiology, Immunology & Molecular Genetics, University of California Los Angeles, Los Angeles, California 90095-7327, United States
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, California 90095-7327, United States
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Abstract
Lactose permease (LacY), a paradigm for the largest family of membrane transport proteins, catalyzes the coupled translocation of a galactoside and a H+ across the cytoplasmic membrane of Escherichia coli (galactoside/H+ symport). One of the most important aspects of the mechanism is the relationship between protonation and binding of the cargo galactopyranoside. In this regard, it has been shown that protonation is required for binding. Furthermore when galactoside affinity is measured as a function of pH, an apparent pK (pKapp) of ∼10.5 is obtained. Strikingly, when Glu325, a residue long known to be involved in coupling between H+ and sugar translocation, is replaced with a neutral side chain, the pH effect is abolished, and high-affinity binding is observed until LacY is destabilized at alkaline pH. In this paper, infrared spectroscopy is used to identify Glu325 in situ. Moreover, it is demonstrated that this residue exhibits a pKa of 10.5 ± 0.1 that is insensitive to the presence of galactopyranoside. Thus, it is apparent that protonation of Glu325 specifically is required for effective sugar binding to LacY.
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