1
|
Chanket W, Pipatthana M, Sangphukieo A, Harnvoravongchai P, Chankhamhaengdecha S, Janvilisri T, Phanchana M. The complete catalog of antimicrobial resistance secondary active transporters in Clostridioides difficile: evolution and drug resistance perspective. Comput Struct Biotechnol J 2024; 23:2358-2374. [PMID: 38873647 PMCID: PMC11170357 DOI: 10.1016/j.csbj.2024.05.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 05/01/2024] [Accepted: 05/16/2024] [Indexed: 06/15/2024] Open
Abstract
Secondary active transporters shuttle substrates across eukaryotic and prokaryotic membranes, utilizing different electrochemical gradients. They are recognized as one of the antimicrobial efflux pumps among pathogens. While primary active transporters within the genome of C. difficile 630 have been completely cataloged, the systematical study of secondary active transporters remains incomplete. Here, we not only identify secondary active transporters but also disclose their evolution and role in drug resistance in C. difficile 630. Our analysis reveals that C. difficile 630 carries 147 secondary active transporters belonging to 27 (super)families. Notably, 50 (34%) of them potentially contribute to antimicrobial resistance (AMR). AMR-secondary active transporters are structurally classified into five (super)families: the p-aminobenzoyl-glutamate transporter (AbgT), drug/metabolite transporter (DMT) superfamily, major facilitator (MFS) superfamily, multidrug and toxic compound extrusion (MATE) family, and resistance-nodulation-division (RND) family. Surprisingly, complete RND genes found in C. difficile 630 are likely an evolutionary leftover from the common ancestor with the diderm. Through protein structure comparisons, we have potentially identified six novel AMR-secondary active transporters from DMT, MATE, and MFS (super)families. Pangenome analysis revealed that half of the AMR-secondary transporters are accessory genes, which indicates an important role in adaptive AMR function rather than innate physiological homeostasis. Gene expression profile firmly supports their ability to respond to a wide spectrum of antibiotics. Our findings highlight the evolution of AMR-secondary active transporters and their integral role in antibiotic responses. This marks AMR-secondary active transporters as interesting therapeutic targets to synergize with other antibiotic activity.
Collapse
Affiliation(s)
- Wannarat Chanket
- Graduate Program in Molecular Medicine, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Methinee Pipatthana
- Department of Microbiology, Faculty of Public Health, Mahidol University, Bangkok, Thailand
| | - Apiwat Sangphukieo
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | | | | | - Tavan Janvilisri
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Matthew Phanchana
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| |
Collapse
|
2
|
Rimon A, Amartely H, Padan E. The crossing of two unwound transmembrane regions that is the hallmark of the NhaA structural fold is critical for antiporter activity. Sci Rep 2024; 14:5915. [PMID: 38467695 PMCID: PMC10928194 DOI: 10.1038/s41598-024-56425-3] [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: 12/06/2023] [Accepted: 03/06/2024] [Indexed: 03/13/2024] Open
Abstract
Cell pH and Na+ homeostasis requires Na+/H+ antiporters. The crystal structure of NhaA, the main Escherichia coli Na+/H+ antiporter, revealed a unique NhaA structural fold shared by prokaryotic and eukaryotic membrane proteins. Out of the 12 NhaA transmembrane segments (TMs), TMs III-V and X-XII are topologically inverted repeats with unwound TMs IV and XI forming the X shape characterizing the NhaA fold. We show that intramolecular cross-linking under oxidizing conditions of a NhaA mutant with two Cys replacements across the crossing (D133C-T340C) inhibits antiporter activity and impairs NhaA-dependent cell growth in high-salts. The affinity purified D133C-T340C protein binds Li+ (the Na+ surrogate substrate of NhaA) under reducing conditions. The cross-linking traps the antiporter in an outward-facing conformation, blocking the antiport cycle. As many secondary transporters are found to share the NhaA fold, including some involved in human diseases, our data have importance for both basic and clinical research.
Collapse
Affiliation(s)
- Abraham Rimon
- Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, Jerusalem, Israel
- The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 91904, Jerusalem, Israel
| | - Hadar Amartely
- Wolfson Center for Applied Structural Biology, Jerusalem, Israel
- The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 91904, Jerusalem, Israel
| | - Etana Padan
- Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, Jerusalem, Israel.
- The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 91904, Jerusalem, Israel.
| |
Collapse
|
3
|
Özkan M, Yılmaz H, Ergenekon P, Erdoğan EM, Erbakan M. Microbial membrane transport proteins and their biotechnological applications. World J Microbiol Biotechnol 2024; 40:71. [PMID: 38225445 PMCID: PMC10789880 DOI: 10.1007/s11274-024-03891-6] [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: 12/01/2023] [Accepted: 01/09/2024] [Indexed: 01/17/2024]
Abstract
Because of the hydrophobic nature of the membrane lipid bilayer, the majority of the hydrophilic solutes require special transportation mechanisms for passing through the cell membrane. Integral membrane transport proteins (MTPs), which belong to the Major Intrinsic Protein Family, facilitate the transport of these solutes across cell membranes. MTPs including aquaporins and carrier proteins are transmembrane proteins spanning across the cell membrane. The easy handling of microorganisms enabled the discovery of a remarkable number of transport proteins specific to different substances. It has been realized that these transporters have very important roles in the survival of microorganisms, their pathogenesis, and antimicrobial resistance. Astonishing features related to the solute specificity of these proteins have led to the acceleration of the research on the discovery of their properties and the development of innovative products in which these unique properties are used or imitated. Studies on microbial MTPs range from the discovery and characterization of a novel transporter protein to the mining and screening of them in a large transporter library for particular functions, from simulations and modeling of specific transporters to the preparation of biomimetic synthetic materials for different purposes such as biosensors or filtration membranes. This review presents recent discoveries on microbial membrane transport proteins and focuses especially on formate nitrite transport proteins and aquaporins, and advances in their biotechnological applications.
Collapse
Affiliation(s)
- Melek Özkan
- Environmental Engineering Department, Gebze Technical University, Kocaeli, 41400, Türkiye.
| | - Hilal Yılmaz
- Environmental Engineering Department, Gebze Technical University, Kocaeli, 41400, Türkiye
| | - Pınar Ergenekon
- Environmental Engineering Department, Gebze Technical University, Kocaeli, 41400, Türkiye
| | - Esra Meşe Erdoğan
- Environmental Engineering Department, Gebze Technical University, Kocaeli, 41400, Türkiye
| | - Mustafa Erbakan
- Biosystem Engineering Department, Bozok University, Yozgat , 66900, Türkiye
| |
Collapse
|
4
|
Trebesch N, Tajkhorshid E. Structure Reveals Homology in Elevator Transporters. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.14.544989. [PMID: 37398459 PMCID: PMC10312693 DOI: 10.1101/2023.06.14.544989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
The elevator transport mechanism is one of the handful of canonical mechanisms by which transporters shuttle their substrates across the semi-permeable membranes that surround cells and organelles. Studies of molecular function are naturally guided by evolutionary context, but until now this context has been limited for elevator transporters because established evolutionary classification methods have organized them into several apparently unrelated families. Through comprehensive examination of the pertinent structures available in the Protein Data Bank, we show that 62 elevator transporters from 18 families share a conserved architecture in their transport domains consisting of 10 helices connected in 8 topologies. Through quantitative analysis of the structural similarity, structural complexity, and topologically-corrected sequence similarity among the transport domains, we provide compelling evidence that these elevator transporters are all homologous. Using our analysis, we have constructed a phylogenetic tree to enable quantification and visualization of the evolutionary relationships among elevator transporters and their families. We also report several examples of functional features that are shared by elevator transporters from different families. Our findings shed new light on the elevator transport mechanism and allow us to understand it in a far deeper and more nuanced manner.
Collapse
Affiliation(s)
- Noah Trebesch
- Theoretical and Computational Biophysics Group, NIH Resource for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Resource for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign
| |
Collapse
|
5
|
Gauthier-Coles G, Fairweather SJ, Bröer A, Bröer S. Do Amino Acid Antiporters Have Asymmetric Substrate Specificity? Biomolecules 2023; 13:biom13020301. [PMID: 36830670 PMCID: PMC9953452 DOI: 10.3390/biom13020301] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/31/2023] [Accepted: 02/03/2023] [Indexed: 02/10/2023] Open
Abstract
Amino acid antiporters mediate the 1:1 exchange of groups of amino acids. Whether substrate specificity can be different for the inward and outward facing conformation has not been investigated systematically, although examples of asymmetric transport have been reported. Here we used LC-MS to detect the movement of 12C- and 13C-labelled amino acid mixtures across the plasma membrane of Xenopus laevis oocytes expressing a variety of amino acid antiporters. Differences of substrate specificity between transporter paralogs were readily observed using this method. Our results suggest that antiporters are largely symmetric, equalizing the pools of their substrate amino acids. Exceptions are the antiporters y+LAT1 and y+LAT2 where neutral amino acids are co-transported with Na+ ions, favouring their import. For the antiporters ASCT1 and ASCT2 glycine acted as a selective influx substrate, while proline was a selective influx substrate of ASCT1. These data show that antiporters can display non-canonical modes of transport.
Collapse
|
6
|
Hu W, Chi C, Song K, Zheng H. The molecular mechanism of sialic acid transport mediated by Sialin. SCIENCE ADVANCES 2023; 9:eade8346. [PMID: 36662855 PMCID: PMC9858498 DOI: 10.1126/sciadv.ade8346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Abstract
Malfunction of the sialic acid transporter caused by various genetic mutations in the SLC17A5 gene encoding Sialin leads to a spectrum of neurodegenerative conditions called free sialic acid storage disorders. Unfortunately, how Sialin transports sialic acid/proton (H+) and how pathogenic mutations impair its function are poorly defined. Here, we present the structure of human Sialin in an inward-facing partially open conformation determined by cryo-electron microscopy, representing the first high-resolution structure of any human SLC17 member. Our analysis reveals two unique features in Sialin: (i) The H+ coupling/sensing requires two highly conserved Glu residues (E171 and E175) instead of one (E175) as implied in previous studies; and (ii) the normal function of Sialin requires the stabilization of a cytosolic helix, which has not been noticed in the literature. By mapping known pathogenic mutations, we provide mechanistic explanations for corresponding functional defects. We propose a structure-based mechanism for sialic acid transport mediated by Sialin.
Collapse
Affiliation(s)
- Wenxin Hu
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, School of Medicine, Aurora, CO, USA
| | - Congwu Chi
- Division of Cardiology, Department of Medicine, University of Colorado Anschutz Medical Campus, School of Medicine, Aurora, CO, USA
| | - Kunhua Song
- Division of Cardiology, Department of Medicine, University of Colorado Anschutz Medical Campus, School of Medicine, Aurora, CO, USA
| | - Hongjin Zheng
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, School of Medicine, Aurora, CO, USA
| |
Collapse
|
7
|
Structure and function of H +/K + pump mutants reveal Na +/K + pump mechanisms. Nat Commun 2022; 13:5270. [PMID: 36085139 PMCID: PMC9463140 DOI: 10.1038/s41467-022-32793-0] [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: 06/07/2022] [Accepted: 08/17/2022] [Indexed: 11/09/2022] Open
Abstract
Ion-transport mechanisms evolve by changing ion-selectivity, such as switching from Na+ to H+ selectivity in secondary-active transporters or P-type-ATPases. Here we study primary-active transport via P-type ATPases using functional and structural analyses to demonstrate that four simultaneous residue substitutions transform the non-gastric H+/K+ pump, a strict H+-dependent electroneutral P-type ATPase, into a bona fide Na+-dependent electrogenic Na+/K+ pump. Conversion of a H+-dependent primary-active transporter into a Na+-dependent one provides a prototype for similar studies of ion-transport proteins. Moreover, we solve the structures of the wild-type non-gastric H+/K+ pump, a suitable drug target to treat cystic fibrosis, and of its Na+/K+ pump-mimicking mutant in two major conformations, providing insight on how Na+ binding drives a concerted mechanism leading to Na+/K+ pump phosphorylation.
Collapse
|
8
|
Abdel-Karim SAAM, El-Ganiny AMA, El-Sayed MA, Abbas HAA. Promising FDA-approved drugs with efflux pump inhibitory activities against clinical isolates of Staphylococcus aureus. PLoS One 2022; 17:e0272417. [PMID: 35905077 PMCID: PMC9337675 DOI: 10.1371/journal.pone.0272417] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 07/19/2022] [Indexed: 12/04/2022] Open
Abstract
Background and objectives Staphylococcus aureus is an opportunistic pathogen that causes wide range of nosocomial and community-acquired infections which have spread worldwide leading to an urgent need for developing effective anti-staphylococcal agents. Efflux is an important resistance mechanism that bacteria used to fight the antimicrobial action. This study aimed to investigate the efflux mechanism in S. aureus and assess diclofenac, domperidone, glyceryl trinitrate and metformin as potential efflux pump inhibitors that can be used in combination with antibiotics for treating topical infections caused by S. aureus. Materials and methods Efflux was detected qualitatively by the ethidium bromide Cart-Wheel method followed by investigating the presence of efflux genes by polymerase chain reaction. Twenty-six isolates were selected for further investigation of efflux by Cart-Wheel method in absence and presence of tested compounds followed by quantitative efflux assay. Furthermore, antibiotics minimum inhibitory concentrations in absence and presence of tested compounds were determined. The effects of tested drugs on expression levels of efflux genes norA, fexA and tetK were determined by quantitative real time-polymerase chain reaction. Results Efflux was found in 65.3% of isolates, the prevalence of norA, tetK, fexA and msrA genes were 91.7%, 77.8%, 27.8% and 6.9%. Efflux assay revealed that tested drugs had potential efflux inhibitory activities, reduced the antibiotic’s MICs and significantly decreased the relative expression of efflux genes. Conclusion Diclofenac sodium, domperidone and glyceryl trinitrate showed higher efflux inhibitory activities than verapamil and metformin. To our knowledge, this is the first report that shows that diclofenac sodium, glyceryl trinitrate and domperidone have efflux pump inhibitory activities against S. aureus.
Collapse
Affiliation(s)
| | | | - Mona Abdelmonem El-Sayed
- Department of Microbiology and Immunology, Faculty of Pharmacy, Zagazig University, Zagazig, Egypt
| | | |
Collapse
|
9
|
Del Alamo D, Meiler J, Mchaourab HS. Principles of Alternating Access in LeuT-fold Transporters: Commonalities and Divergences. J Mol Biol 2022; 434:167746. [PMID: 35843285 DOI: 10.1016/j.jmb.2022.167746] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 07/08/2022] [Accepted: 07/09/2022] [Indexed: 11/15/2022]
Abstract
Found in all domains of life, transporters belonging to the LeuT-fold class mediate the import and exchange of hydrophilic and charged compounds such as amino acids, metals, and sugar molecules. Nearly two decades of investigations on the eponymous bacterial transporter LeuT have yielded a library of high-resolution snapshots of its conformational cycle linked by solution-state experimental data obtained from multiple techniques. In parallel, its topology has been observed in symporters and antiporters characterized by a spectrum of substrate specificities and coupled to gradients of distinct ions. Here we review and compare mechanistic models of transport for LeuT, its well-studied homologs, as well as functionally distant members of the fold, emphasizing the commonalities and divergences in alternating access and the corresponding energy landscapes. Our integrated summary illustrates how fold conservation, a hallmark of the LeuT fold, coincides with divergent choreographies of alternating access that nevertheless capitalize on recurrent structural motifs. In addition, it highlights the knowledge gap that hinders the leveraging of the current body of research into detailed mechanisms of transport for this important class of membrane proteins.
Collapse
Affiliation(s)
- Diego Del Alamo
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA; Department of Chemistry, Vanderbilt University, Nashville, TN, USA. https://twitter.com/DdelAlamo
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA; Institute for Drug Discovery, Leipzig University, Leipzig, DE, USA. https://twitter.com/MeilerLab
| | - Hassane S Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA.
| |
Collapse
|
10
|
Berlaga A, Kolomeisky AB. Understanding Mechanisms of Secondary Active Transport by Analyzing the Effects of Mutations and Stoichiometry. J Phys Chem Lett 2022; 13:5405-5412. [PMID: 35679158 DOI: 10.1021/acs.jpclett.2c01232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Biological cells frequently exhibit a so-called secondary active transport by moving various species across their membranes. In this mode of transport, an energetically favorable transmembrane gradient of one type of molecule is used to drive another type of molecule in the energetically unfavorable direction against their gradient. Although it is well established that conformational transitions play a critical role in functioning of transporters, the molecular details of underlying mechanisms remain not well understood. Here, we utilize a recently developed theoretical method to understand better the microscopic picture of secondary active transport. Specifically, we evaluate how mutations in different parts of transporters affect their dynamic properties. In addition, we present a possible explanation on existence of different stoichiometries in the secondary active transport. Our theoretical analysis clarifies several important aspects of complex biological transport phenomena.
Collapse
Affiliation(s)
- Alex Berlaga
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
| | - Anatoly B Kolomeisky
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, United States
- Department of Physics and Astronomy, Rice University, Houston, Texas 77005, United States
| |
Collapse
|
11
|
Beckstein O, Naughton F. General principles of secondary active transporter function. BIOPHYSICS REVIEWS 2022; 3:011307. [PMID: 35434715 PMCID: PMC8984959 DOI: 10.1063/5.0047967] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 02/23/2022] [Indexed: 04/13/2023]
Abstract
Transport of ions and small molecules across the cell membrane against electrochemical gradients is catalyzed by integral membrane proteins that use a source of free energy to drive the energetically uphill flux of the transported substrate. Secondary active transporters couple the spontaneous influx of a "driving" ion such as Na+ or H+ to the flux of the substrate. The thermodynamics of such cyclical non-equilibrium systems are well understood, and recent work has focused on the molecular mechanism of secondary active transport. The fact that these transporters change their conformation between an inward-facing and outward-facing conformation in a cyclical fashion, called the alternating access model, is broadly recognized as the molecular framework in which to describe transporter function. However, only with the advent of high resolution crystal structures and detailed computer simulations, it has become possible to recognize common molecular-level principles between disparate transporter families. Inverted repeat symmetry in secondary active transporters has shed light onto how protein structures can encode a bi-stable two-state system. Based on structural data, three broad classes of alternating access transitions have been described as rocker-switch, rocking-bundle, and elevator mechanisms. More detailed analysis indicates that transporters can be understood as gated pores with at least two coupled gates. These gates are not just a convenient cartoon element to illustrate a putative mechanism but map to distinct parts of the transporter protein. Enumerating all distinct gate states naturally includes occluded states in the alternating access picture and also suggests what kind of protein conformations might be observable. By connecting the possible conformational states and ion/substrate bound states in a kinetic model, a unified picture emerges in which the symporter, antiporter, and uniporter functions are extremes in a continuum of functionality. As usual with biological systems, few principles and rules are absolute and exceptions are discussed as well as how biological complexity may be integrated in quantitative kinetic models that may provide a bridge from the structure to function.
Collapse
Affiliation(s)
- Oliver Beckstein
- Department of Physics, Arizona State University, Tempe, Arizona 85287, USA
| | | |
Collapse
|
12
|
Berlaga A, Kolomeisky AB. Theoretical study of active secondary transport: Unexpected differences in molecular mechanisms for antiporters and symporters. J Chem Phys 2022; 156:085102. [DOI: 10.1063/5.0082589] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Successful functioning of biological cells relies on efficient translocation of different materials across cellular membranes. An important part of this transportation system is membrane channels that are known as antiporters and symporters. They exploit the energy stored as a trans-membrane gradient of one type of molecules to transport the other types of molecules against their gradients. For symporters, the directions of both fluxes for driving and driven species coincide, while for antiporters, the fluxes move in opposite directions. There are surprising experimental observations that despite differing only by the direction of transport fluxes, the molecular mechanisms of translocation adopted by antiporters and symporters seem to be drastically different. We present chemical-kinetic models to quantitatively investigate this phenomenon. Our theoretical approach allows us to explain why antiporters mostly utilize a single-site transportation when only one molecule of any type might be associated with the channel. At the same time, the transport in symporters requires two molecules of different types to be simultaneously associated with the channel. In addition, we investigate the kinetic constraints and efficiency of symporters and compare them with the same properties of antiporters. Our theoretical analysis clarifies some important physical–chemical features of cellular trans-membrane transport.
Collapse
Affiliation(s)
- Alex Berlaga
- Department of Chemistry, Rice University, Houston, Texas 77005, USA
| | - Anatoly B. Kolomeisky
- Department of Chemistry and Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, USA
| |
Collapse
|
13
|
Li J, Sae Her A, Traaseth NJ. Asymmetric protonation of glutamate residues drives a preferred transport pathway in EmrE. Proc Natl Acad Sci U S A 2021; 118:e2110790118. [PMID: 34607959 PMCID: PMC8521673 DOI: 10.1073/pnas.2110790118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/20/2021] [Indexed: 11/18/2022] Open
Abstract
EmrE is an Escherichia coli multidrug efflux pump and member of the small multidrug resistance (SMR) family that transports drugs as a homodimer by harnessing energy from the proton motive force. SMR family transporters contain a conserved glutamate residue in transmembrane 1 (Glu14 in EmrE) that is required for binding protons and drugs. Yet the mechanism underlying proton-coupled transport by the two glutamate residues in the dimer remains unresolved. Here, we used NMR spectroscopy to determine acid dissociation constants (pKa ) for wild-type EmrE and heterodimers containing one or two Glu14 residues in the dimer. For wild-type EmrE, we measured chemical shifts of the carboxyl side chain of Glu14 using solid-state NMR in lipid bilayers and obtained unambiguous evidence on the existence of asymmetric protonation states. Subsequent measurements of pKa values for heterodimers with a single Glu14 residue showed no significant differences from heterodimers with two Glu14 residues, supporting a model where the two Glu14 residues have independent pKa values and are not electrostatically coupled. These insights support a transport pathway with well-defined protonation states in each monomer of the dimer, including a preferred cytoplasmic-facing state where Glu14 is deprotonated in monomer A and protonated in monomer B under pH conditions in the cytoplasm of E. coli Our findings also lead to a model, hop-free exchange, which proposes how exchangers with conformation-dependent pKa values reduce proton leakage. This model is relevant to the SMR family and transporters comprised of inverted repeat domains.
Collapse
Affiliation(s)
- Jianping Li
- Department of Chemistry, New York University, New York, NY 10003
| | - Ampon Sae Her
- Department of Chemistry, New York University, New York, NY 10003
| | | |
Collapse
|
14
|
Dvorak V, Wiedmer T, Ingles-Prieto A, Altermatt P, Batoulis H, Bärenz F, Bender E, Digles D, Dürrenberger F, Heitman LH, IJzerman AP, Kell DB, Kickinger S, Körzö D, Leippe P, Licher T, Manolova V, Rizzetto R, Sassone F, Scarabottolo L, Schlessinger A, Schneider V, Sijben HJ, Steck AL, Sundström H, Tremolada S, Wilhelm M, Wright Muelas M, Zindel D, Steppan CM, Superti-Furga G. An Overview of Cell-Based Assay Platforms for the Solute Carrier Family of Transporters. Front Pharmacol 2021; 12:722889. [PMID: 34447313 PMCID: PMC8383457 DOI: 10.3389/fphar.2021.722889] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 07/19/2021] [Indexed: 12/12/2022] Open
Abstract
The solute carrier (SLC) superfamily represents the biggest family of transporters with important roles in health and disease. Despite being attractive and druggable targets, the majority of SLCs remains understudied. One major hurdle in research on SLCs is the lack of tools, such as cell-based assays to investigate their biological role and for drug discovery. Another challenge is the disperse and anecdotal information on assay strategies that are suitable for SLCs. This review provides a comprehensive overview of state-of-the-art cellular assay technologies for SLC research and discusses relevant SLC characteristics enabling the choice of an optimal assay technology. The Innovative Medicines Initiative consortium RESOLUTE intends to accelerate research on SLCs by providing the scientific community with high-quality reagents, assay technologies and data sets, and to ultimately unlock SLCs for drug discovery.
Collapse
Affiliation(s)
- Vojtech Dvorak
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Tabea Wiedmer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Alvaro Ingles-Prieto
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | | | - Helena Batoulis
- Drug Discovery Sciences–Lead Discovery, Bayer Pharmaceuticals, Wuppertal, Germany
| | - Felix Bärenz
- Sanofi-Aventis Deutschland GmbH, Frankfurt am Main, Germany
| | - Eckhard Bender
- Drug Discovery Sciences–Lead Discovery, Bayer Pharmaceuticals, Wuppertal, Germany
| | - Daniela Digles
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | | | - Laura H. Heitman
- Division of Drug Discovery and Safety, LACDR, Leiden University, Leiden, Netherlands
| | - Adriaan P. IJzerman
- Division of Drug Discovery and Safety, LACDR, Leiden University, Leiden, Netherlands
| | - Douglas B. Kell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Stefanie Kickinger
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Daniel Körzö
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Philipp Leippe
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Thomas Licher
- Sanofi-Aventis Deutschland GmbH, Frankfurt am Main, Germany
| | | | | | | | | | - Avner Schlessinger
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Vanessa Schneider
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Hubert J. Sijben
- Division of Drug Discovery and Safety, LACDR, Leiden University, Leiden, Netherlands
| | | | | | | | | | - Marina Wright Muelas
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Diana Zindel
- Drug Discovery Sciences–Lead Discovery, Bayer Pharmaceuticals, Wuppertal, Germany
| | - Claire M. Steppan
- Pfizer Worldwide Research, Development and Medical, Groton, MA, United States
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| |
Collapse
|
15
|
Sudha G, Bassot C, Lamb J, Shu N, Huang Y, Elofsson A. The evolutionary history of topological variations in the CPA/AT transporters. PLoS Comput Biol 2021; 17:e1009278. [PMID: 34403419 PMCID: PMC8396727 DOI: 10.1371/journal.pcbi.1009278] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 08/27/2021] [Accepted: 07/14/2021] [Indexed: 11/23/2022] Open
Abstract
CPA/AT transporters are made up of scaffold and a core domain. The core domain contains two non-canonical helices (broken or reentrant) that mediate the transport of ions, amino acids or other charged compounds. During evolution, these transporters have undergone substantial changes in structure, topology and function. To shed light on these structural transitions, we create models for all families using an integrated topology annotation method. We find that the CPA/AT transporters can be classified into four fold-types based on their structure; (1) the CPA-broken fold-type, (2) the CPA-reentrant fold-type, (3) the BART fold-type, and (4) a previously not described fold-type, the Reentrant-Helix-Reentrant fold-type. Several topological transitions are identified, including the transition between a broken and reentrant helix, one transition between a loop and a reentrant helix, complete changes of orientation, and changes in the number of scaffold helices. These transitions are mainly caused by gene duplication and shuffling events. Structural models, topology information and other details are presented in a searchable database, CPAfold (cpafold.bioinfo.se).
Collapse
Affiliation(s)
- Govindarajan Sudha
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Claudio Bassot
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - John Lamb
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Nanjiang Shu
- Bioinformatics Short-term Support and Infrastructure (BILS), Science for Life Laboratory, Sweden
| | - Yan Huang
- Science for Life Laboratory, Karolinska Institutet, Stockholm University, Solna, Sweden
| | - Arne Elofsson
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| |
Collapse
|
16
|
ActTRANS: Functional classification in active transport proteins based on transfer learning and contextual representations. Comput Biol Chem 2021; 93:107537. [PMID: 34217007 DOI: 10.1016/j.compbiolchem.2021.107537] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 05/09/2021] [Accepted: 06/26/2021] [Indexed: 01/08/2023]
Abstract
MOTIVATION Primary and secondary active transport are two types of active transport that involve using energy to move the substances. Active transport mechanisms do use proteins to assist in transport and play essential roles to regulate the traffic of ions or small molecules across a cell membrane against the concentration gradient. In this study, the two main types of proteins involved in such transport are classified from transmembrane transport proteins. We propose a Support Vector Machine (SVM) with contextualized word embeddings from Bidirectional Encoder Representations from Transformers (BERT) to represent protein sequences. BERT is a powerful model in transfer learning, a deep learning language representation model developed by Google and one of the highest performing pre-trained model for Natural Language Processing (NLP) tasks. The idea of transfer learning with pre-trained model from BERT is applied to extract fixed feature vectors from the hidden layers and learn contextual relations between amino acids in the protein sequence. Therefore, the contextualized word representations of proteins are introduced to effectively model complex structures of amino acids in the sequence and the variations of these amino acids in the context. By generating context information, we capture multiple meanings for the same amino acid to reveal the importance of specific residues in the protein sequence. RESULTS The performance of the proposed method is evaluated using five-fold cross-validation and independent test. The proposed method achieves an accuracy of 85.44 %, 88.74 % and 92.84 % for Class-1, Class-2, and Class-3, respectively. Experimental results show that this approach can outperform from other feature extraction methods using context information, effectively classify two types of active transport and improve the overall performance.
Collapse
|
17
|
Del Alamo D, Govaerts C, Mchaourab HS. AlphaFold2 predicts the inward-facing conformation of the multidrug transporter LmrP. Proteins 2021; 89:1226-1228. [PMID: 33973689 DOI: 10.1002/prot.26138] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/18/2021] [Accepted: 05/03/2021] [Indexed: 01/30/2023]
Abstract
As part of the CASP competition, the protein structure prediction algorithm AlphaFold2 generated multiple models of the proton/drug antiporter LmrP. Previous distance restraints from double electron-electron resonance spectroscopy, a technique which reports distance distributions between spin labels attached to proteins, suggest that one of the lower-ranked models may have captured a conformation that has so far eluded experimental structure determination.
Collapse
Affiliation(s)
- Diego Del Alamo
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
| | - Cédric Govaerts
- Laboratory for the Structure and Function of Biological Membranes, Center for Structural Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium
| | - Hassane S Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
| |
Collapse
|
18
|
Molecular Mechanism of Nramp-Family Transition Metal Transport. J Mol Biol 2021; 433:166991. [PMID: 33865868 DOI: 10.1016/j.jmb.2021.166991] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 04/02/2021] [Accepted: 04/05/2021] [Indexed: 02/06/2023]
Abstract
The Natural resistance-associated macrophage protein (Nramp) family of transition metal transporters enables uptake and trafficking of essential micronutrients that all organisms must acquire to survive. Two decades after Nramps were identified as proton-driven, voltage-dependent secondary transporters, multiple Nramp crystal structures have begun to illustrate the fine details of the transport process and provide a new framework for understanding a wealth of preexisting biochemical data. Here we review the relevant literature pertaining to Nramps' biological roles and especially their conserved molecular mechanism, including our updated understanding of conformational change, metal binding and transport, substrate selectivity, proton transport, proton-metal coupling, and voltage dependence. We ultimately describe how the Nramp family has adapted the LeuT fold common to many secondary transporters to provide selective transition-metal transport with a mechanism that deviates from the canonical model of symport.
Collapse
|
19
|
Carusela MF, Miguel Rubi J. Computational Model for Membrane Transporters. Potential Implications for Cancer. Front Cell Dev Biol 2021; 9:642665. [PMID: 33693005 PMCID: PMC7937797 DOI: 10.3389/fcell.2021.642665] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/04/2021] [Indexed: 01/13/2023] Open
Abstract
To explain the increased transport of nutrients and metabolites and to control the movement of drug molecules through the transporters to the cancer cells, it is important to understand the exact mechanism of their structure and activity, as well as their biological and physical characteristics. We propose a computational model that reproduces the functionality of membrane transporters by quantifying the flow of substrates through the cell membrane. The model identifies the force induced by conformational changes of the transporter due to hydrolysis of ATP, in ABC transporters, or by an electrochemical gradient of ions, in secondary transporters. The transport rate is computed by averaging the velocity generated by the force along the paths followed by the substrates. The results obtained are in accordance with the experiments. The model provides an overall framework for analyzing the membrane transport proteins that regulate the flows of ions, nutrients and other molecules across the cell membranes, and their activities.
Collapse
Affiliation(s)
- María Florencia Carusela
- Instituto de Ciencias, Universidad Nacional de General Sarmiento, Buenos Aires, Argentina
- National Scientific and Technical Research Council, Buenos Aires, Argentina
| | - J. Miguel Rubi
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, Barcelona, Spain
| |
Collapse
|
20
|
Matin TR, Heath GR, Huysmans GHM, Boudker O, Scheuring S. Millisecond dynamics of an unlabeled amino acid transporter. Nat Commun 2020; 11:5016. [PMID: 33024106 PMCID: PMC7538599 DOI: 10.1038/s41467-020-18811-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 09/16/2020] [Indexed: 12/14/2022] Open
Abstract
Excitatory amino acid transporters (EAATs) are important in many physiological processes and crucial for the removal of excitatory amino acids from the synaptic cleft. Here, we develop and apply high-speed atomic force microscopy line-scanning (HS-AFM-LS) combined with automated state assignment and transition analysis for the determination of transport dynamics of unlabeled membrane-reconstituted GltPh, a prokaryotic EAAT homologue, with millisecond temporal resolution. We find that GltPh transporters can operate much faster than previously reported, with state dwell-times in the 50 ms range, and report the kinetics of an intermediate transport state with height between the outward- and inward-facing states. Transport domains stochastically probe transmembrane motion, and reversible unsuccessful excursions to the intermediate state occur. The presented approach and analysis methodology are generally applicable to study transporter kinetics at system-relevant temporal resolution. Excitatory amino acid transporters (EAATs) are crucial for the removal of excitatory amino acids from the synaptic cleft. Here authors combined high-speed atomic force microscopy line-scanning with automated state assignment for the determination of transport dynamics of GltPh, a prokaryotic EAAT homologue, with millisecond temporal resolution.
Collapse
Affiliation(s)
- Tina R Matin
- Department of Anesthesiology, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA.,Department of Physiology and Biophysics, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - George R Heath
- Department of Anesthesiology, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA.,Department of Physiology and Biophysics, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Gerard H M Huysmans
- Department of Physiology and Biophysics, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Olga Boudker
- Department of Physiology and Biophysics, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA.,Howard Hughes Medical Institute, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Simon Scheuring
- Department of Anesthesiology, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA. .,Department of Physiology and Biophysics, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA.
| |
Collapse
|
21
|
Babst M. Regulation of nutrient transporters by metabolic and environmental stresses. Curr Opin Cell Biol 2020; 65:35-41. [PMID: 32200208 DOI: 10.1016/j.ceb.2020.02.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 02/15/2020] [Indexed: 12/17/2022]
Abstract
The yeast plasma membrane is a selective barrier between an erratic environment and the cell's metabolism. Nutrient transporters are the gatekeepers that control the import of molecules feeding into the metabolic pathways. Nutrient import adjusts rapidly to changes in metabolism and the environment, which is accomplished by regulating the surface expression of transporters. Recent studies indicate that the lipid environment in which transporters function regulates ubiquitination efficiency and endocytosis of these proteins. Changes in the lipid environment are caused by lateral movements of the transporters between different membrane domains and by the influence of the extracellular environment on the fluidity of the plasma membrane.
Collapse
Affiliation(s)
- Markus Babst
- Henry Eyring Center for Cell and Genome Science, University of Utah, Salt Lake City, UT 84112, USA.
| |
Collapse
|
22
|
Onyeabor M, Martinez R, Kurgan G, Wang X. Engineering transport systems for microbial production. ADVANCES IN APPLIED MICROBIOLOGY 2020; 111:33-87. [PMID: 32446412 DOI: 10.1016/bs.aambs.2020.01.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The rapid development in the field of metabolic engineering has enabled complex modifications of metabolic pathways to generate a diverse product portfolio. Manipulating substrate uptake and product export is an important research area in metabolic engineering. Optimization of transport systems has the potential to enhance microbial production of renewable fuels and chemicals. This chapter comprehensively reviews the transport systems critical for microbial production as well as current genetic engineering strategies to improve transport functions and thus production metrics. In addition, this chapter highlights recent advancements in engineering microbial efflux systems to enhance cellular tolerance to industrially relevant chemical stress. Lastly, future directions to address current technological gaps are discussed.
Collapse
Affiliation(s)
- Moses Onyeabor
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Rodrigo Martinez
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Gavin Kurgan
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Xuan Wang
- School of Life Sciences, Arizona State University, Tempe, AZ, United States.
| |
Collapse
|
23
|
Góral I, Łątka K, Bajda M. Structure Modeling of the Norepinephrine Transporter. Biomolecules 2020; 10:E102. [PMID: 31936154 PMCID: PMC7022499 DOI: 10.3390/biom10010102] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 12/31/2019] [Accepted: 01/03/2020] [Indexed: 01/09/2023] Open
Abstract
The norepinephrine transporter (NET) is one of the monoamine transporters. Its X-ray crystal structure has not been obtained yet. Inhibitors of human NET (hNET) play a major role in the treatment of many central and peripheral nervous system diseases. In this study, we focused on the spatial structure of a NET constructed by homology modeling on Drosophila melanogaster dopamine transporter templates. We further examined molecular construction of primary binding pocket (S1) together with secondary binding site (S2) and extracellular loop 4 (EL4). The next stage involved docking of transporter inhibitors: Reboxetine, duloxetine, desipramine, and other commonly used drugs. The procedure revealed the molecular orientation of residues and disclosed ones that are the most important for ligand binding: Phenylalanine F72, aspartic acid D75, tyrosine Y152, and phenylalanine F317. Aspartic acid D75 plays a key role in recognition of the basic amino group present in monoamine transporter inhibitors and substrates. The study also presents a comparison of hNET models with other related proteins, which could provide new insights into their interaction with therapeutics and aid future development of novel bioactive compounds.
Collapse
Affiliation(s)
| | | | - Marek Bajda
- Department of Physicochemical Drug Analysis, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688 Cracow, Poland; (I.G.); (K.Ł.)
| |
Collapse
|
24
|
Li J, Zhao Z, Tajkhorshid E. Locking Two Rigid-body Bundles in an Outward-Facing Conformation: The Ion-coupling Mechanism in a LeuT-fold Transporter. Sci Rep 2019; 9:19479. [PMID: 31862903 PMCID: PMC6925253 DOI: 10.1038/s41598-019-55722-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 12/02/2019] [Indexed: 01/26/2023] Open
Abstract
Secondary active transporters use electrochemical gradient of ions to fuel the "uphill" translocation of the substrate following the alternating-access model. The coupling of ions to conformational dynamics of the protein remains one of the least characterized aspects of the transporter function. We employ extended molecular dynamics (MD) simulations to examine the Na+-binding effects on the structure and dynamics of a LeuT-fold, Na+-coupled secondary transporter (Mhp1) in its major conformational states, i.e., the outward-facing (OF) and inward-facing (IF) states, as well as on the OF ↔ IF state transition. Microsecond-long, unbiased MD simulations illustrate that Na+ stabilizes an OF conformation favorable for substrate association, by binding to a highly conserved site at the interface between the two helical bundles and restraining their relative position and motion. Furthermore, a special-protocol biased simulation for state transition suggests that Na+ binding hinders the OF ↔ IF transition. These synergistic Na+-binding effects allosterically couple the ion and substrate binding sites and modify the kinetics of state transition, collectively increasing the lifetime of an OF conformation with high substrate affinity, thereby facilitating substrate recruitment from a low-concentration environment. Based on the similarity between our findings for Mhp1 and experimental reports on LeuT, we propose that this model may represent a general Na+-coupling mechanism among LeuT-fold transporters.
Collapse
Affiliation(s)
- Jing Li
- NIH Center for Macromolecular Modeling and Bioinformatics, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, United States
| | - Zhiyu Zhao
- NIH Center for Macromolecular Modeling and Bioinformatics, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States
| | - Emad Tajkhorshid
- NIH Center for Macromolecular Modeling and Bioinformatics, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States.
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States.
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States.
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States.
| |
Collapse
|
25
|
Zhou W, Fiorin G, Anselmi C, Karimi-Varzaneh HA, Poblete H, Forrest LR, Faraldo-Gómez JD. Large-scale state-dependent membrane remodeling by a transporter protein. eLife 2019; 8:50576. [PMID: 31855177 PMCID: PMC6957315 DOI: 10.7554/elife.50576] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 12/17/2019] [Indexed: 12/22/2022] Open
Abstract
That channels and transporters can influence the membrane morphology is increasingly recognized. Less appreciated is that the extent and free-energy cost of these deformations likely varies among different functional states of a protein, and thus, that they might contribute significantly to defining its mechanism. We consider the trimeric Na+-aspartate symporter GltPh, a homolog of an important class of neurotransmitter transporters, whose mechanism entails one of the most drastic structural changes known. Molecular simulations indicate that when the protomers become inward-facing, they cause deep, long-ranged, and yet mutually-independent membrane deformations. Using a novel simulation methodology, we estimate that the free-energy cost of this membrane perturbation is in the order of 6–7 kcal/mol per protomer. Compensating free-energy contributions within the protein or its environment must thus stabilize this inward-facing conformation for the transporter to function. We discuss these striking results in the context of existing experimental observations for this and other transporters.
Collapse
Affiliation(s)
- Wenchang Zhou
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Giacomo Fiorin
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Claudio Anselmi
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Hossein Ali Karimi-Varzaneh
- Computational Structural Biology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, United States
| | - Horacio Poblete
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, United States.,Computational Structural Biology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, United States
| | - Lucy R Forrest
- Computational Structural Biology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, United States
| | - José D Faraldo-Gómez
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, United States
| |
Collapse
|
26
|
Bozzi AT, Bane LB, Zimanyi CM, Gaudet R. Unique structural features in an Nramp metal transporter impart substrate-specific proton cotransport and a kinetic bias to favor import. J Gen Physiol 2019; 151:1413-1429. [PMID: 31619456 PMCID: PMC6888756 DOI: 10.1085/jgp.201912428] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 09/26/2019] [Indexed: 01/01/2023] Open
Abstract
Natural resistance-associated macrophage protein (Nramp) transporters enable uptake of essential transition metal micronutrients in numerous biological contexts. These proteins are believed to function as secondary transporters that harness the electrochemical energy of proton gradients by "coupling" proton and metal transport. Here we use the Deinococcus radiodurans (Dra) Nramp homologue, for which we have determined crystal structures in multiple conformations, to investigate mechanistic details of metal and proton transport. We untangle the proton-metal coupling behavior of DraNramp into two distinct phenomena: ΔpH stimulation of metal transport rates and metal stimulation of proton transport. Surprisingly, metal type influences substrate stoichiometry, leading to manganese-proton cotransport but cadmium uniport, while proton uniport also occurs. Additionally, a physiological negative membrane potential is required for high-affinity metal uptake. To begin to understand how Nramp's structure imparts these properties, we target a conserved salt-bridge network that forms a proton-transport pathway from the metal-binding site to the cytosol. Mutations to this network diminish voltage and ΔpH dependence of metal transport rates, alter substrate selectivity, perturb or eliminate metal-stimulated proton transport, and erode the directional bias favoring outward-to-inward metal transport under physiological-like conditions. Thus, this unique salt-bridge network may help Nramp-family transporters maximize metal uptake and reduce deleterious back-transport of acquired metals. We provide a new mechanistic model for Nramp proton-metal cotransport and propose that functional advantages may arise from deviations from the traditional model of symport.
Collapse
Affiliation(s)
- Aaron T Bozzi
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA
| | - Lukas B Bane
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA
| | - Christina M Zimanyi
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA
| | - Rachelle Gaudet
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA
| |
Collapse
|
27
|
Structure of the mannose transporter of the bacterial phosphotransferase system. Cell Res 2019; 29:680-682. [PMID: 31209249 DOI: 10.1038/s41422-019-0194-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 05/14/2019] [Indexed: 12/17/2022] Open
|
28
|
Babst M. Eisosomes at the intersection of TORC1 and TORC2 regulation. Traffic 2019; 20:543-551. [PMID: 31038844 DOI: 10.1111/tra.12651] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 04/24/2019] [Accepted: 04/26/2019] [Indexed: 12/14/2022]
Abstract
Eisosomes are furrows in the yeast plasma membrane that form a membrane domain with distinct lipid and protein composition. Recent studies highlighted the importance of this domain for the regulation of proton-nutrient symporters. The amino acids and other nutrients, which these transporters deliver to the cytoplasm not only feed into metabolic pathways but also activate the metabolic regulator TORC1. Eisosomes have also been shown to harbor the membrane stress sensors Slm1 and Slm2. Membrane tension caused by hypoosmotic shock results in the redistribution of Slm1/2 from eisosomes to TORC2 which in turn regulates lipid synthesis. Therefore, eisosomes function upstream of both TORC1 and TORC2 regulation.
Collapse
Affiliation(s)
- Markus Babst
- Henry Eyring Center for Cell and Genome Science, University of Utah, Salt Lake City, Utah
| |
Collapse
|
29
|
Kuk ACY, Hao A, Guan Z, Lee SY. Visualizing conformation transitions of the Lipid II flippase MurJ. Nat Commun 2019; 10:1736. [PMID: 30988294 PMCID: PMC6465408 DOI: 10.1038/s41467-019-09658-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 03/22/2019] [Indexed: 02/06/2023] Open
Abstract
The biosynthesis of many polysaccharides, including bacterial peptidoglycan and eukaryotic N-linked glycans, requires transport of lipid-linked oligosaccharide (LLO) precursors across the membrane by specialized flippases. MurJ is the flippase for the lipid-linked peptidoglycan precursor Lipid II, a key player in bacterial cell wall synthesis, and a target of recently discovered antibacterials. However, the flipping mechanism of LLOs including Lipid II remains poorly understood due to a dearth of structural information. Here we report crystal structures of MurJ captured in inward-closed, inward-open, inward-occluded and outward-facing conformations. Together with mutagenesis studies, we elucidate the conformational transitions in MurJ that mediate lipid flipping, identify the key ion for function, and provide a framework for the development of inhibitors. MurJ is the flippase for the lipid-linked peptidoglycan precursor Lipid II, a key player in bacterial cell wall synthesis, but the flipping mechanism remains poorly understood. Here authors report crystal structures of MurJ in different conformations which shed light on the MurJ transitions that mediate lipid flipping.
Collapse
Affiliation(s)
- Alvin C Y Kuk
- Department of Biochemistry, Duke University Medical Center, 303 Research Drive, Durham, NC, 27710, USA
| | - Aili Hao
- Department of Biochemistry, Duke University Medical Center, 303 Research Drive, Durham, NC, 27710, USA
| | - Ziqiang Guan
- Department of Biochemistry, Duke University Medical Center, 303 Research Drive, Durham, NC, 27710, USA
| | - Seok-Yong Lee
- Department of Biochemistry, Duke University Medical Center, 303 Research Drive, Durham, NC, 27710, USA.
| |
Collapse
|
30
|
Leone V, Waclawska I, Kossmann K, Koshy C, Sharma M, Prisner TF, Ziegler C, Endeward B, Forrest LR. Interpretation of spectroscopic data using molecular simulations for the secondary active transporter BetP. J Gen Physiol 2019; 151:381-394. [PMID: 30728216 PMCID: PMC6400524 DOI: 10.1085/jgp.201812111] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 11/26/2018] [Accepted: 01/11/2019] [Indexed: 11/20/2022] Open
Abstract
Mechanistic understanding of dynamic membrane proteins such as transporters, receptors, and channels requires accurate depictions of conformational ensembles, and the manner in which they interchange as a function of environmental factors including substrates, lipids, and inhibitors. Spectroscopic techniques such as electron spin resonance (ESR) pulsed electron-electron double resonance (PELDOR), also known as double electron-electron resonance (DEER), provide a complement to atomistic structures obtained from x-ray crystallography or cryo-EM, since spectroscopic data reflect an ensemble and can be measured in more native solvents, unperturbed by a crystal lattice. However, attempts to interpret DEER data are frequently stymied by discrepancies with the structural data, which may arise due to differences in conditions, the dynamics of the protein, or the flexibility of the attached paramagnetic spin labels. Recently, molecular simulation techniques such as EBMetaD have been developed that create a conformational ensemble matching an experimental distance distribution while applying the minimal possible bias. Moreover, it has been proposed that the work required during an EBMetaD simulation to match an experimentally determined distribution could be used as a metric with which to assign conformational states to a given measurement. Here, we demonstrate the application of this concept for a sodium-coupled transport protein, BetP. Because the probe, protein, and lipid bilayer are all represented in atomic detail, the different contributions to the work, such as the extent of protein backbone movements, can be separated. This work therefore illustrates how ranking simulations based on EBMetaD can help to bridge the gap between structural and biophysical data and thereby enhance our understanding of membrane protein conformational mechanisms.
Collapse
Affiliation(s)
- Vanessa Leone
- Computational Structural Biology Section, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
| | | | - Katharina Kossmann
- Institute of Biophysics and Biophysical Chemistry, University of Regensburg, Regensburg, Germany
| | - Caroline Koshy
- Max Planck Institute for Biophysics, Frankfurt am Main, Germany
| | - Monika Sharma
- Computational Structural Biology Section, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
| | - Thomas F Prisner
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University, Frankfurt am Main, Germany
| | - Christine Ziegler
- Institute of Biophysics and Biophysical Chemistry, University of Regensburg, Regensburg, Germany
| | - Burkhard Endeward
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University, Frankfurt am Main, Germany
| | - Lucy R Forrest
- Computational Structural Biology Section, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
| |
Collapse
|
31
|
Bozzi AT, Zimanyi CM, Nicoludis JM, Lee BK, Zhang CH, Gaudet R. Structures in multiple conformations reveal distinct transition metal and proton pathways in an Nramp transporter. eLife 2019; 8:41124. [PMID: 30714568 PMCID: PMC6398981 DOI: 10.7554/elife.41124] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 01/31/2019] [Indexed: 01/03/2023] Open
Abstract
Nramp family transporters—expressed in organisms from bacteria to humans—enable uptake of essential divalent transition metals via an alternating-access mechanism that also involves proton transport. We present high-resolution structures of Deinococcus radiodurans (Dra)Nramp in multiple conformations to provide a thorough description of the Nramp transport cycle by identifying the key intramolecular rearrangements and changes to the metal coordination sphere. Strikingly, while metal transport requires cycling from outward- to inward-open states, efficient proton transport still occurs in outward-locked (but not inward-locked) DraNramp. We propose a model in which metal and proton enter the transporter via the same external pathway to the binding site, but follow separate routes to the cytoplasm, which could facilitate the co-transport of two cationic species. Our results illustrate the flexibility of the LeuT fold to support a broad range of substrate transport and conformational change mechanisms. Cells use transport proteins embedded in their membrane to acquire many of the nutrients they need to survive and grow. Different transport proteins transport different nutrients; for example, the Nramp transporters move transition metal ions across cell membranes. Nramps are found in a wide range of organisms. Bacteria use them to acquire the metals they need during the course of an infection, and humans rely on Nramps to absorb iron from food. Nramps can also transport hydrogen ions (known as protons). Understanding how the structure of an Nramp transporter changes as it transports metal ions and protons can help researchers to understand how it works. These structures can be studied using a technique called X-ray crystallography, which captures snapshots of the proteins at different stages of their task. Bozzi, Zimanyi et al. used X-ray crystallography to study the structures of an Nramp transporter from the bacterium Deinococcus radiodurans. The results reveal four of the shapes that the Nramp transporter takes on at different stages in its transport process, including the first structure to show an Nramp binding to a metal ion from the outside of the cell. Taken together, the structures suggest a new transport mechanism that has not been seen in previously studied transport proteins with similar structures. An unexpected feature of this mechanism is that Nramps transport metal ions and protons along different pathways. Studying the transport mechanisms used by Nramp transporters will help researchers to understand how cells maintain appropriate levels of metal ions, an important component of human health. The mechanisms of relatively few transport proteins are understood at a structural level, yet many share common origins and have shared characteristics. Understanding how Nramps work could therefore help us to understand how wider classes of transporters work as well.
Collapse
Affiliation(s)
- Aaron T Bozzi
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Christina M Zimanyi
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - John M Nicoludis
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Brandon K Lee
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Casey H Zhang
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Rachelle Gaudet
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| |
Collapse
|
32
|
Thomas NE, Wu C, Morrison EA, Robinson AE, Werner JP, Henzler-Wildman KA. The C terminus of the bacterial multidrug transporter EmrE couples drug binding to proton release. J Biol Chem 2018; 293:19137-19147. [PMID: 30287687 DOI: 10.1074/jbc.ra118.005430] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 09/25/2018] [Indexed: 01/16/2023] Open
Abstract
Ion-coupled transporters must regulate access of ions and substrates into and out of the binding site to actively transport substrates and minimize dissipative leak of ions. Within the single-site alternating access model, competitive substrate binding forms the foundation of ion-coupled antiport. Strict competition between substrates leads to stoichiometric antiport without slippage. However, recent NMR studies of the bacterial multidrug transporter EmrE have demonstrated that this multidrug transporter can simultaneously bind drug and proton, which will affect the transport stoichiometry and efficiency of coupled antiport. Here, we investigated the nature of substrate competition in EmrE using multiple methods to measure proton release upon the addition of saturating concentrations of drug as a function of pH. The resulting proton-release profile confirmed simultaneous binding of drug and proton, but suggested that a residue outside EmrE's Glu-14 binding site may release protons upon drug binding. Using NMR-monitored pH titrations, we trace this drug-induced deprotonation event to His-110, EmrE's C-terminal residue. Further NMR experiments disclosed that the C-terminal tail is strongly coupled to EmrE's drug-binding domain. Consideration of our results alongside those from previous studies of EmrE suggests that this conserved tail participates in secondary gating of EmrE-mediated proton/drug transport, occluding the binding pocket of fully protonated EmrE in the absence of drug to prevent dissipative proton transport.
Collapse
Affiliation(s)
- Nathan E Thomas
- From the Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706 and
| | - Chao Wu
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Emma A Morrison
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Anne E Robinson
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Josephine P Werner
- From the Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706 and
| | - Katherine A Henzler-Wildman
- From the Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706 and .,Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110
| |
Collapse
|
33
|
Majumder P, Mallela AK, Penmatsa A. Transporters through the looking glass. An insight into the mechanisms of ion-coupled transport and methods that help reveal them. J Indian Inst Sci 2018; 98:283-300. [PMID: 30686879 PMCID: PMC6345361 DOI: 10.1007/s41745-018-0081-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 06/05/2018] [Indexed: 12/18/2022]
Abstract
Cell membranes, despite providing a barrier to protect intracellular constituents, require selective gating for influx of important metabolites including ions, sugars, amino acids, neurotransmitters and efflux of toxins and metabolic end-products. The machinery involved in carrying out this gating process comprises of integral membrane proteins that use ionic electrochemical gradients or ATP hydrolysis, to drive concentrative uptake or efflux. The mechanism through which ion-coupled transporters function is referred to as alternating-access. In the recent past, discrete modes of alternating-access have been described with the elucidation of new transporter structures and their snapshots in altered conformational states. Despite X-ray structures being the primary sources of mechanistic information, other biophysical methods provide information related to the structural dynamics of these transporters. Methods including EPR and smFRET, have extensively helped validate or clarify ion-coupled transport mechanisms, in a near-native environment. This review seeks to highlight the mechanistic details of ion-coupled transport and delve into the biophysical tools and methods that help in understanding these fascinating molecules.
Collapse
Affiliation(s)
- Puja Majumder
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012 India
| | | | - Aravind Penmatsa
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012 India
| |
Collapse
|
34
|
Palazzolo L, Parravicini C, Laurenzi T, Guerrini U, Indiveri C, Gianazza E, Eberini I. In silico Description of LAT1 Transport Mechanism at an Atomistic Level. Front Chem 2018; 6:350. [PMID: 30197880 PMCID: PMC6117385 DOI: 10.3389/fchem.2018.00350] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 07/25/2018] [Indexed: 11/24/2022] Open
Abstract
The molecular mechanism of transport mediated by LAT1, a sodium-independent antiporter of large neutral amino acids, was investigated through in silico procedures, specifically making reference to two transported substrates, tyrosine (Tyr) and leucine methyl ester (LME), and to 3,5-diiodo-L-tyrosine (DIT), a well-known LAT1 inhibitor. Two models of the transporter were built by comparative modeling, with LAT1 either in an outward-facing (OF) or in an inward-facing (IF) conformation, based, respectively, on the crystal structure of AdiC and of GadC. As frequently classic Molecular Dynamics (MD) fails to monitor large-scale conformational transitions within a reasonable simulated time, the OF structure was equilibrated for 150 ns then processed through targeted MD (tMD). During this procedure, an elastic force pulled the OF structure to the IF structure and induced, at the same time, substrates/inhibitor to move through the transport channel. This elastic force was modulated by a spring constant (k) value; by decreasing its value from 100 to 70, it was possible to comparatively account for the propensity for transport of the three tested molecules. In line with our expectations, during the tMD simulations, Tyr and LME behaved as substrates, moving down the transport channel, or most of it, for all k values. On the contrary, DIT behaved as an inhibitor, being (almost) transported across the channel only at the highest k value (100). During their transit through the channel, Tyr and LME interacted with specific amino acids (first with Phe252 then with Thr345, Arg348, Tyr259, and Phe262); this suggests that a primary as well as a putative secondary gate may contribute to the transport of substrates. Quite on the opposite, DIT appeared to establish only transient interactions with side chains lining the external part of the transport channel. Our tMD simulations could thus efficiently discriminate between two transported substrates and one inhibitor, and therefore can be proposed as a benchmark for developing novel LAT1 inhibitors of pharmacological interest.
Collapse
Affiliation(s)
- Luca Palazzolo
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Chiara Parravicini
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Tommaso Laurenzi
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Uliano Guerrini
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Cesare Indiveri
- Dipartimento di Biologia, Ecologia e Scienze della Terra, University of Calabria, Cosenza, Italy
| | - Elisabetta Gianazza
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Ivano Eberini
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| |
Collapse
|
35
|
Luo P, Dai S, Zeng J, Duan J, Shi H, Wang J. Inward-facing conformation of l-ascorbate transporter suggests an elevator mechanism. Cell Discov 2018; 4:35. [PMID: 30038796 PMCID: PMC6048161 DOI: 10.1038/s41421-018-0037-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 05/03/2018] [Accepted: 05/08/2018] [Indexed: 11/09/2022] Open
Abstract
Various bacteria can ferment vitamin C (l-ascorbate) under anaerobic conditions via the phosphoenolpyruvate-dependent phosphotransferase system (PTS). The PTSasc system is composed of two soluble energy-coupling proteins (EI and HPr) and an enzyme II complex (EIIA, EIIB, and EIIC) for the anaerobic uptake of ascorbate and its phosphorylation to l-ascorbate 6-phosphate in vivo. Crystal structures of the ascorbate-bound EIIC component from Escherichia coli are available in outward-open and occluded conformations, suggesting a possible elevator mechanism of membrane transport. Despite these advances, it remains unclear how EIIC actually transports the substrate across the membrane and interacts with EIIB, which transfers its phosphate group to the EIIC-embedding ascorbate. Here, we present the crystal structure of the EIICasc component from Pasteurella multocida in the inward-facing conformation. By comparing three conformational states, we confirmed the original proposed model: the ascorbate translocation can be achieved by a rigid-body movement of the substrate-binding core domain relative to the V motif domain, which brings along the transmembrane helices TM2 and TM7 of the V motif domain to undergo a winding at the pivotal positions. Together with an in vivo transport assay, we completed the picture of the transport cycle of the ascorbate superfamily of membrane-spanning EIIC components of the PTS system.
Collapse
Affiliation(s)
- Ping Luo
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Shuliu Dai
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Jianwei Zeng
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Jinsong Duan
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Hui Shi
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Jiawei Wang
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| |
Collapse
|
36
|
Hayashi MK. Structure-Function Relationship of Transporters in the Glutamate-Glutamine Cycle of the Central Nervous System. Int J Mol Sci 2018; 19:ijms19041177. [PMID: 29649168 PMCID: PMC5979278 DOI: 10.3390/ijms19041177] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 04/09/2018] [Accepted: 04/10/2018] [Indexed: 12/12/2022] Open
Abstract
Many kinds of transporters contribute to glutamatergic excitatory synaptic transmission. Glutamate is loaded into synaptic vesicles by vesicular glutamate transporters to be released from presynaptic terminals. After synaptic vesicle release, glutamate is taken up by neurons or astrocytes to terminate the signal and to prepare for the next signal. Glutamate transporters on the plasma membrane are responsible for transporting glutamate from extracellular fluid to cytoplasm. Glutamate taken up by astrocyte is converted to glutamine by glutamine synthetase and transported back to neurons through glutamine transporters on the plasma membranes of the astrocytes and then on neurons. Glutamine is converted back to glutamate by glutaminase in the neuronal cytoplasm and then loaded into synaptic vesicles again. Here, the structures of glutamate transporters and glutamine transporters, their conformational changes, and how they use electrochemical gradients of various ions for substrate transport are summarized. Pharmacological regulations of these transporters are also discussed.
Collapse
Affiliation(s)
- Mariko Kato Hayashi
- School of Medicine, International University of Health and Welfare, 4-3 Kozunomori, Narita, Chiba 286-8686, Japan.
| |
Collapse
|
37
|
Structural basis for the alternating access mechanism of the cation diffusion facilitator YiiP. Proc Natl Acad Sci U S A 2018; 115:3042-3047. [PMID: 29507252 DOI: 10.1073/pnas.1715051115] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
YiiP is a dimeric antiporter from the cation diffusion facilitator family that uses the proton motive force to transport Zn2+ across bacterial membranes. Previous work defined the atomic structure of an outward-facing conformation, the location of several Zn2+ binding sites, and hydrophobic residues that appear to control access to the transport sites from the cytoplasm. A low-resolution cryo-EM structure revealed changes within the membrane domain that were associated with the alternating access mechanism for transport. In the current work, the resolution of this cryo-EM structure has been extended to 4.1 Å. Comparison with the X-ray structure defines the differences between inward-facing and outward-facing conformations at an atomic level. These differences include rocking and twisting of a four-helix bundle that harbors the Zn2+ transport site and controls its accessibility within each monomer. As previously noted, membrane domains are closely associated in the dimeric structure from cryo-EM but dramatically splayed apart in the X-ray structure. Cysteine crosslinking was used to constrain these membrane domains and to show that this large-scale splaying was not necessary for transport activity. Furthermore, dimer stability was not compromised by mutagenesis of elements in the cytoplasmic domain, suggesting that the extensive interface between membrane domains is a strong determinant of dimerization. As with other secondary transporters, this interface could provide a stable scaffold for movements of the four-helix bundle that confers alternating access of these ions to opposite sides of the membrane.
Collapse
|
38
|
Pinu FR, Granucci N, Daniell J, Han TL, Carneiro S, Rocha I, Nielsen J, Villas-Boas SG. Metabolite secretion in microorganisms: the theory of metabolic overflow put to the test. Metabolomics 2018; 14:43. [PMID: 30830324 DOI: 10.1007/s11306-018-1339-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 02/07/2018] [Indexed: 12/24/2022]
Abstract
INTRODUCTION Microbial cells secrete many metabolites during growth, including important intermediates of the central carbon metabolism. This has not been taken into account by researchers when modeling microbial metabolism for metabolic engineering and systems biology studies. MATERIALS AND METHODS The uptake of metabolites by microorganisms is well studied, but our knowledge of how and why they secrete different intracellular compounds is poor. The secretion of metabolites by microbial cells has traditionally been regarded as a consequence of intracellular metabolic overflow. CONCLUSIONS Here, we provide evidence based on time-series metabolomics data that microbial cells eliminate some metabolites in response to environmental cues, independent of metabolic overflow. Moreover, we review the different mechanisms of metabolite secretion and explore how this knowledge can benefit metabolic modeling and engineering.
Collapse
Affiliation(s)
- Farhana R Pinu
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand.
| | - Ninna Granucci
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - James Daniell
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
- LanzaTech, Skokie, IL, 60077, USA
| | - Ting-Li Han
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Sonia Carneiro
- Center of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Isabel Rocha
- Center of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivagen 10, 412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970, Hørsholm, Denmark
| | - Silas G Villas-Boas
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| |
Collapse
|
39
|
Lekshmi M, Ammini P, Adjei J, Sanford LM, Shrestha U, Kumar S, Varela MF. Modulation of antimicrobial efflux pumps of the major facilitator superfamily in Staphylococcus aureus. AIMS Microbiol 2018; 4:1-18. [PMID: 31294201 PMCID: PMC6605029 DOI: 10.3934/microbiol.2018.1.1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 12/19/2017] [Indexed: 12/15/2022] Open
Abstract
Variants of the microorganism Staphylococcus aureus which are resistant to antimicrobial agents exist as causative agents of serious infectious disease and constitute a considerable public health concern. One of the main antimicrobial resistance mechanisms harbored by S. aureus pathogens is exemplified by integral membrane transport systems that actively remove antimicrobial agents from bacteria where the cytoplasmic drug targets reside, thus allowing the bacteria to survive and grow. An important class of solute transporter proteins, called the major facilitator superfamily, includes related and homologous passive and secondary active transport systems, many of which are antimicrobial efflux pumps. Transporters of the major facilitator superfamily, which confer antimicrobial efflux and bacterial resistance in S. aureus, are good targets for development of resistance-modifying agents, such as efflux pump inhibition. Such modulatory action upon these antimicrobial efflux systems of the major facilitator superfamily in S. aureus may circumvent resistance and restore the clinical efficacy of therapy towards S. aureus infection.
Collapse
Affiliation(s)
- Manjusha Lekshmi
- QC Laboratory, Harvest and Post Harvest Technology Division, ICAR-Central Institute of Fisheries Education (CIFE), Seven Bungalows, Versova, Andheri (W), Mumbai, 400061, India
| | - Parvathi Ammini
- CSIR-National Institute of Oceanography (NIO), Regional Centre, Dr. Salim Ali Road, Kochi, 682018, India
| | - Jones Adjei
- Eastern New Mexico, Department of Biology, Station 33, 1500 South Avenue K, Portales, NM, 88130, USA
| | - Leslie M Sanford
- Eastern New Mexico, Department of Biology, Station 33, 1500 South Avenue K, Portales, NM, 88130, USA
| | - Ugina Shrestha
- Eastern New Mexico, Department of Biology, Station 33, 1500 South Avenue K, Portales, NM, 88130, USA
| | - Sanath Kumar
- QC Laboratory, Harvest and Post Harvest Technology Division, ICAR-Central Institute of Fisheries Education (CIFE), Seven Bungalows, Versova, Andheri (W), Mumbai, 400061, India
| | - Manuel F Varela
- Eastern New Mexico, Department of Biology, Station 33, 1500 South Avenue K, Portales, NM, 88130, USA
| |
Collapse
|
40
|
Calabrese AN, Jackson SM, Jones LN, Beckstein O, Heinkel F, Gsponer J, Sharples D, Sans M, Kokkinidou M, Pearson AR, Radford SE, Ashcroft AE, Henderson PJF. Topological Dissection of the Membrane Transport Protein Mhp1 Derived from Cysteine Accessibility and Mass Spectrometry. Anal Chem 2017; 89:8844-8852. [PMID: 28726379 PMCID: PMC5588088 DOI: 10.1021/acs.analchem.7b01310] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Accepted: 07/20/2017] [Indexed: 01/01/2023]
Abstract
Cys accessibility and quantitative intact mass spectrometry (MS) analyses have been devised to study the topological transitions of Mhp1, the membrane protein for sodium-linked transport of hydantoins from Microbacterium liquefaciens. Mhp1 has been crystallized in three forms (outward-facing open, outward-facing occluded with substrate bound, and inward-facing open). We show that one natural cysteine residue, Cys327, out of three, has an enhanced solvent accessibility in the inward-facing (relative to the outward-facing) form. Reaction of the purified protein, in detergent, with the thiol-reactive N-ethylmalemide (NEM), results in modification of Cys327, suggesting that Mhp1 adopts predominantly inward-facing conformations. Addition of either sodium ions or the substrate 5-benzyl-l-hydantoin (L-BH) does not shift this conformational equilibrium, but systematic co-addition of the two results in an attenuation of labeling, indicating a shift toward outward-facing conformations that can be interpreted using conventional enzyme kinetic analyses. Such measurements can afford the Km for each ligand as well as the stoichiometry of ion-substrate-coupled conformational changes. Mutations that perturb the substrate binding site either result in the protein being unable to adopt outward-facing conformations or in a global destabilization of structure. The methodology combines covalent labeling, mass spectrometry, and kinetic analyses in a straightforward workflow applicable to a range of systems, enabling the interrogation of changes in a protein's conformation required for function at varied concentrations of substrates, and the consequences of mutations on these conformational transitions.
Collapse
Affiliation(s)
| | | | | | - Oliver Beckstein
- Department of Physics, Arizona State University , Tempe, Arizona 85287-1504, United States
| | - Florian Heinkel
- Centre for High-Throughput Biology, University of British Columbia , Vancouver, British Columbia, Canada V6T 1Z4
| | - Joerg Gsponer
- Centre for High-Throughput Biology, University of British Columbia , Vancouver, British Columbia, Canada V6T 1Z4
| | | | - Marta Sans
- Hamburg Centre for Ultrafast Imaging, Institute for Nanostructure and Solid State Physics, Universität Hamburg , Hamburg 22761, Germany
| | - Maria Kokkinidou
- Hamburg Centre for Ultrafast Imaging, Institute for Nanostructure and Solid State Physics, Universität Hamburg , Hamburg 22761, Germany
| | - Arwen R Pearson
- Hamburg Centre for Ultrafast Imaging, Institute for Nanostructure and Solid State Physics, Universität Hamburg , Hamburg 22761, Germany
| | | | | | | |
Collapse
|
41
|
Lewinson O, Livnat-Levanon N. Mechanism of Action of ABC Importers: Conservation, Divergence, and Physiological Adaptations. J Mol Biol 2017; 429:606-619. [PMID: 28104364 DOI: 10.1016/j.jmb.2017.01.010] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 01/03/2017] [Accepted: 01/04/2017] [Indexed: 01/08/2023]
Abstract
The past decade has seen a remarkable surge in structural characterization of ATP binding cassette (ABC) transporters, which have spurred a more focused functional analysis of these elaborate molecular machines. As a result, it has become increasingly apparent that there is a substantial degree of mechanistic variation between ABC transporters that function as importers, which correlates with their physiological roles. Here, we summarize recent advances in ABC importers' structure-function studies and provide an explanation as to the origin of the different mechanisms of action.
Collapse
Affiliation(s)
- Oded Lewinson
- Department of Biochemistry, The Bruce and Ruth Rappaport Faculty of Medicine, The Technion-Israel Institute of Technology, 31096 Haifa, Israel.
| | - Nurit Livnat-Levanon
- Department of Biochemistry, The Bruce and Ruth Rappaport Faculty of Medicine, The Technion-Israel Institute of Technology, 31096 Haifa, Israel
| |
Collapse
|
42
|
Marron AO, Ratcliffe S, Wheeler GL, Goldstein RE, King N, Not F, de Vargas C, Richter DJ. The Evolution of Silicon Transport in Eukaryotes. Mol Biol Evol 2016; 33:3226-3248. [PMID: 27729397 PMCID: PMC5100055 DOI: 10.1093/molbev/msw209] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Biosilicification (the formation of biological structures from silica) occurs in diverse eukaryotic lineages, plays a major role in global biogeochemical cycles, and has significant biotechnological applications. Silicon (Si) uptake is crucial for biosilicification, yet the evolutionary history of the transporters involved remains poorly known. Recent evidence suggests that the SIT family of Si transporters, initially identified in diatoms, may be widely distributed, with an extended family of related transporters (SIT-Ls) present in some nonsilicified organisms. Here, we identify SITs and SIT-Ls in a range of eukaryotes, including major silicified lineages (radiolarians and chrysophytes) and also bacterial SIT-Ls. Our evidence suggests that the symmetrical 10-transmembrane-domain SIT structure has independently evolved multiple times via duplication and fusion of 5-transmembrane-domain SIT-Ls. We also identify a second gene family, similar to the active Si transporter Lsi2, that is broadly distributed amongst siliceous and nonsiliceous eukaryotes. Our analyses resolve a distinct group of Lsi2-like genes, including plant and diatom Si-responsive genes, and sequences unique to siliceous sponges and choanoflagellates. The SIT/SIT-L and Lsi2 transporter families likely contribute to biosilicification in diverse lineages, indicating an ancient role for Si transport in eukaryotes. We propose that these Si transporters may have arisen initially to prevent Si toxicity in the high Si Precambrian oceans, with subsequent biologically induced reductions in Si concentrations of Phanerozoic seas leading to widespread losses of SIT, SIT-L, and Lsi2-like genes in diverse lineages. Thus, the origin and diversification of two independent Si transporter families both drove and were driven by ancient ocean Si levels.
Collapse
Affiliation(s)
- Alan O Marron
- Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Cambridge, United Kingdom .,Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Sarah Ratcliffe
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, University Walk, Bristol, United Kingdom
| | - Glen L Wheeler
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth, Devon, United Kingdom
| | - Raymond E Goldstein
- Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Nicole King
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, CA
| | - Fabrice Not
- CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, France.,Sorbonne Universités, Université Pierre et Marie Curie (UPMC) Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, France
| | - Colomban de Vargas
- CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, France.,Sorbonne Universités, Université Pierre et Marie Curie (UPMC) Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, France
| | - Daniel J Richter
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, CA.,CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, France.,Sorbonne Universités, Université Pierre et Marie Curie (UPMC) Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, France
| |
Collapse
|
43
|
Zhang JL, Zheng QC, Yu LY, Li ZQ, Zhang HX. Effect of External Electric Field on Substrate Transport of a Secondary Active Transporter. J Chem Inf Model 2016; 56:1539-46. [PMID: 27472561 DOI: 10.1021/acs.jcim.6b00212] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Substrate transport across a membrane accomplished by a secondary active transporter (SAT) is essential to the normal physiological function of living cells. In the present research, a series of all-atom molecular dynamics (MD) simulations under different electric field (EF) strengths was performed to investigate the effect of an external EF on the substrate transport of an SAT. The results show that EF both affects the interaction between substrate and related protein's residues by changing their conformations and tunes the timeline of the transport event, which collectively reduces the height of energy barrier for substrate transport and results in the appearance of two intermediate conformations under the existence of an external EF. Our work spotlights the crucial influence of external EFs on the substrate transport of SATs and could provide a more penetrating understanding of the substrate transport mechanism of SATs.
Collapse
Affiliation(s)
- Ji-Long Zhang
- International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Institute of Theoretical Chemistry, Jilin University , Changchun 130023, Jilin, People's Republic of China.,Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, Jilin University , Changchun 130021, Jilin, People's Republic of China.,Department of Chemistry and Supercomputing Institute, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Qing-Chuan Zheng
- International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Institute of Theoretical Chemistry, Jilin University , Changchun 130023, Jilin, People's Republic of China
| | - Li-Ying Yu
- International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Institute of Theoretical Chemistry, Jilin University , Changchun 130023, Jilin, People's Republic of China
| | - Zheng-Qiang Li
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, Jilin University , Changchun 130021, Jilin, People's Republic of China
| | - Hong-Xing Zhang
- International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Institute of Theoretical Chemistry, Jilin University , Changchun 130023, Jilin, People's Republic of China
| |
Collapse
|
44
|
Unveiling the Mechanism of Arginine Transport through AdiC with Molecular Dynamics Simulations: The Guiding Role of Aromatic Residues. PLoS One 2016; 11:e0160219. [PMID: 27482712 PMCID: PMC4970712 DOI: 10.1371/journal.pone.0160219] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 07/17/2016] [Indexed: 11/19/2022] Open
Abstract
Commensal and pathogenic enteric bacteria have developed several systems to adapt to proton leakage into the cytoplasm resulting from extreme acidic conditions. One such system involves arginine uptake followed by export of the decarboxylated product agmatine, carried out by the arginine/agmatine antiporter (AdiC), which thus works as a virtual proton pump. Here, using classical and targeted molecular dynamics, we investigated at the atomic level the mechanism of arginine transport through AdiC of E. coli. Overall, our MD simulation data clearly demonstrate that global rearrangements of several transmembrane segments are necessary but not sufficient for achieving transitions between structural states along the arginine translocation pathway. In particular, local structural changes, namely rotameric conversions of two aromatic residues, are needed to regulate access to both the outward- and inward-facing states. Our simulations have also enabled identification of a few residues, overwhelmingly aromatic, which are essential to guiding arginine in the course of its translocation. Most of them belong to gating elements whose coordinated motions contribute to the alternating access mechanism. Their conservation in all known E. coli acid resistance antiporters suggests that the transport mechanisms of these systems share common features. Last but not least, knowledge of the functional properties of AdiC can advance our understanding of the members of the amino acid-carbocation-polyamine superfamily, notably in eukaryotic cells.
Collapse
|
45
|
Czerny DD, Padmanaban S, Anishkin A, Venema K, Riaz Z, Sze H. Protein architecture and core residues in unwound α-helices provide insights to the transport function of plant AtCHX17. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1983-1998. [PMID: 27179641 DOI: 10.1016/j.bbamem.2016.05.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 04/13/2016] [Accepted: 05/08/2016] [Indexed: 01/27/2023]
Abstract
Using Arabidopsis thaliana AtCHX17 as an example, we combine structural modeling and mutagenesis to provide insights on its protein architecture and transport function which is poorly characterized. This approach is based on the observation that protein structures are significantly more conserved in evolution than linear sequences, and mechanistic similarities among diverse transporters are emerging. Two homology models of AtCHX17 were obtained that show a protein fold similar to known structures of bacterial Na(+)/H(+) antiporters, EcNhaA and TtNapA. The distinct secondary and tertiary structure models highlighted residues at positions potentially important for CHX17 activity. Mutagenesis showed that asparagine-N200 and aspartate-D201 inside transmembrane5 (TM5), and lysine-K355 inside TM10 are critical for AtCHX17 activity. We reveal previously unrecognized threonine-T170 and lysine-K383 as key residues at unwound regions in the middle of TM4 and TM11 α-helices, respectively. Mutation of glutamate-E111 located near the membrane surface inhibited AtCHX17 activity, suggesting a role in pH sensing. The long carboxylic tail of unknown purpose has an alternating β-sheet and α-helix secondary structure that is conserved in prokaryote universal stress proteins. These results support the overall architecture of AtCHX17 and identify D201, N200 and novel residues T170 and K383 at the functional core which likely participates in ion recognition, coordination and/or translocation, similar to characterized cation/H(+) exchangers. The core of AtCHX17 models according to EcNhaA and TtNapA templates faces inward and outward, respectively, which may reflect two conformational states of the alternating access transport mode for proteins belonging to the plant CHX family.
Collapse
Affiliation(s)
- Daniel D Czerny
- Department of Cell Biology and Molecular Genetics (DC, SP, ZR, HS), University of Maryland, College Park, MD 20742, USA
| | - Senthilkumar Padmanaban
- Department of Cell Biology and Molecular Genetics (DC, SP, ZR, HS), University of Maryland, College Park, MD 20742, USA
| | - Andriy Anishkin
- Department of Biology, University of Maryland, College Park, MD 20742, USA
| | - Kees Venema
- Dpto de Bioquímica, Biología Celular y Molecular de Plantas, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, c/. Profesor Albareda 1, 18008Granada, Spain
| | - Zoya Riaz
- Department of Cell Biology and Molecular Genetics (DC, SP, ZR, HS), University of Maryland, College Park, MD 20742, USA
| | - Heven Sze
- Department of Cell Biology and Molecular Genetics (DC, SP, ZR, HS), University of Maryland, College Park, MD 20742, USA; Maryland Agricultural Experiment Station, Department of Plant Science and Landscape Architecture (HS), University of Maryland, College Park, MD 20742, USA.
| |
Collapse
|
46
|
Giladi M, Almagor L, van Dijk L, Hiller R, Man P, Forest E, Khananshvili D. Asymmetric Preorganization of Inverted Pair Residues in the Sodium-Calcium Exchanger. Sci Rep 2016; 6:20753. [PMID: 26876271 PMCID: PMC4753433 DOI: 10.1038/srep20753] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 01/07/2016] [Indexed: 01/22/2023] Open
Abstract
In analogy with many other proteins, Na+/Ca2+ exchangers (NCX) adapt an inverted twofold symmetry of repeated structural elements, while exhibiting a functional asymmetry by stabilizing an outward-facing conformation. Here, structure-based mutant analyses of the Methanococcus jannaschii Na+/Ca2+ exchanger (NCX_Mj) were performed in conjunction with HDX-MS (hydrogen/deuterium exchange mass spectrometry) to identify the structure-dynamic determinants of functional asymmetry. HDX-MS identified hallmark differences in backbone dynamics at ion-coordinating residues of apo-NCX_Mj, whereas Na+or Ca2+ binding to the respective sites induced relatively small, but specific, changes in backbone dynamics. Mutant analysis identified ion-coordinating residues affecting the catalytic capacity (kcat/Km), but not the stability of the outward-facing conformation. In contrast, distinct “noncatalytic” residues (adjacent to the ion-coordinating residues) control the stability of the outward-facing conformation, but not the catalytic capacity. The helix-breaking signature sequences (GTSLPE) on the α1 and α2 repeats (at the ion-binding core) differ in their folding/unfolding dynamics, while providing asymmetric contributions to transport activities. The present data strongly support the idea that asymmetric preorganization of the ligand-free ion-pocket predefines catalytic reorganization of ion-bound residues, where secondary interactions with adjacent residues couple the alternating access. These findings provide a structure-dynamic basis for ion-coupled alternating access in NCX and similar proteins.
Collapse
Affiliation(s)
- Moshe Giladi
- Department of Physiology and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Ramat-Aviv 69978, Israel
| | - Lior Almagor
- Department of Physiology and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Ramat-Aviv 69978, Israel
| | - Liat van Dijk
- Department of Physiology and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Ramat-Aviv 69978, Israel
| | - Reuben Hiller
- Department of Physiology and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Ramat-Aviv 69978, Israel
| | - Petr Man
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Eric Forest
- Univ. Grenoble Alpes, IBS, F-38044 Grenoble, France.,CNRS, IBS, F-38044 Grenoble, France.,CEA, IBS, F-38044 Grenoble, France
| | - Daniel Khananshvili
- Department of Physiology and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Ramat-Aviv 69978, Israel
| |
Collapse
|
47
|
|
48
|
Vergara-Jaque A, Fenollar-Ferrer C, Kaufmann D, Forrest LR. Repeat-swap homology modeling of secondary active transporters: updated protocol and prediction of elevator-type mechanisms. Front Pharmacol 2015; 6:183. [PMID: 26388773 PMCID: PMC4560100 DOI: 10.3389/fphar.2015.00183] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 08/13/2015] [Indexed: 12/04/2022] Open
Abstract
Secondary active transporters are critical for neurotransmitter clearance and recycling during synaptic transmission and uptake of nutrients. These proteins mediate the movement of solutes against their concentration gradients, by using the energy released in the movement of ions down pre-existing concentration gradients. To achieve this, transporters conform to the so-called alternating-access hypothesis, whereby the protein adopts at least two conformations in which the substrate binding sites are exposed to one or other side of the membrane, but not both simultaneously. Structures of a bacterial homolog of neuronal glutamate transporters, GltPh, in several different conformational states have revealed that the protein structure is asymmetric in the outward- and inward-open states, and that the conformational change connecting them involves a elevator-like movement of a substrate binding domain across the membrane. The structural asymmetry is created by inverted-topology repeats, i.e., structural repeats with similar overall folds whose transmembrane topologies are related to each other by two-fold pseudo-symmetry around an axis parallel to the membrane plane. Inverted repeats have been found in around three-quarters of secondary transporter folds. Moreover, the (a)symmetry of these systems has been successfully used as a bioinformatic tool, called “repeat-swap modeling” to predict structural models of a transporter in one conformation using the known structure of the transporter in the complementary conformation as a template. Here, we describe an updated repeat-swap homology modeling protocol, and calibrate the accuracy of the method using GltPh, for which both inward- and outward-facing conformations are known. We then apply this repeat-swap homology modeling procedure to a concentrative nucleoside transporter, VcCNT, which has a three-dimensional arrangement related to that of GltPh. The repeat-swapped model of VcCNT predicts that nucleoside transport also occurs via an elevator-like mechanism.
Collapse
Affiliation(s)
- Ariela Vergara-Jaque
- Computational Structural Biology Section, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke - National Institutes of Health, Bethesda, MD USA
| | - Cristina Fenollar-Ferrer
- Computational Structural Biology Section, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke - National Institutes of Health, Bethesda, MD USA
| | - Desirée Kaufmann
- Computational Structural Biology Section, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke - National Institutes of Health, Bethesda, MD USA
| | - Lucy R Forrest
- Computational Structural Biology Section, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke - National Institutes of Health, Bethesda, MD USA
| |
Collapse
|
49
|
Crystal structure of a phosphorylation-coupled vitamin C transporter. Nat Struct Mol Biol 2015; 22:238-41. [PMID: 25686089 DOI: 10.1038/nsmb.2975] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Accepted: 01/14/2015] [Indexed: 12/16/2022]
Abstract
Bacteria use vitamin C (L-ascorbic acid) as a carbon source under anaerobic conditions. The phosphoenolpyruvate-dependent phosphotransferase system (PTS), comprising a transporter (UlaA), a IIB-like enzyme (UlaB) and a IIA-like enzyme (UlaC), is required for the anaerobic uptake of vitamin C and its phosphorylation to L-ascorbate 6-phosphate. Here, we present the crystal structures of vitamin C-bound UlaA from Escherichia coli in two conformations at 1.65-Å and 2.35-Å resolution. UlaA forms a homodimer and exhibits a new fold. Each UlaA protomer consists of 11 transmembrane segments arranged into a 'V-motif' domain and a 'core' domain. The V motifs form the interface between the two protomers, and the core-domain residues coordinate vitamin C. The alternating access of the substrate from the opposite side of the cell membrane may be achieved through rigid-body rotation of the core relative to the V motif.
Collapse
|
50
|
Lee Y, Nishizawa T, Yamashita K, Ishitani R, Nureki O. Structural basis for the facilitative diffusion mechanism by SemiSWEET transporter. Nat Commun 2015; 6:6112. [PMID: 25598322 PMCID: PMC4309421 DOI: 10.1038/ncomms7112] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 12/15/2014] [Indexed: 02/07/2023] Open
Abstract
SWEET family proteins mediate sugar transport across biological membranes and play crucial roles in plants and animals. The SWEETs and their bacterial homologues, the SemiSWEETs, are related to the PQ-loop family, which is characterized by highly conserved proline and glutamine residues (PQ-loop motif). Although the structures of the bacterial SemiSWEETs were recently reported, the conformational transition and the significance of the conserved motif in the transport cycle have remained elusive. Here we report crystal structures of SemiSWEET from Escherichia coli, in the both inward-open and outward-open states. A structural comparison revealed that SemiSWEET undergoes an intramolecular conformational change in each protomer. The conserved PQ-loop motif serves as a molecular hinge that enables the 'binder clip-like' motion of SemiSWEET. The present work provides the framework for understanding the overall transport cycles of SWEET and PQ-loop family proteins.
Collapse
Affiliation(s)
- Yongchan Lee
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Tomohiro Nishizawa
- 1] Department of Biological Sciences, Graduate School of Science, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan [2] Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | | | - Ryuichiro Ishitani
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| |
Collapse
|