1
|
Hariharan P, Guan L. Reconstitution of the Melibiose Permease of Salmonella enterica serovar Typhimurium (MelB St) into Lipid Nanodiscs. Bio Protoc 2024; 14:e5045. [PMID: 39131193 PMCID: PMC11309958 DOI: 10.21769/bioprotoc.5045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 07/03/2024] [Accepted: 07/04/2024] [Indexed: 08/13/2024] Open
Abstract
Membrane proteins play critical roles in cell physiology and pathology. The conventional way to study membrane proteins at protein levels is to use optimal detergents to extract proteins from membranes. Identification of the optimal detergent is tedious , and in some cases, the protein functions are compromised. While this detergent-based approach has produced meaningful results in membrane protein research, a lipid environment should be more suitable to recapture the protein's native folding and functions. This protocol describes how to prepare amphipathic membrane scaffold-proteins (MSPs)-based nanodiscs of a cation-coupled melibiose symporter of Salmonella enterica serovar Typhimurium (MelBSt), a member of the major facilitator superfamily. MSPs generate nano-assemblies containing membrane proteins surrounded by a patch of native lipids to better preserve their native conformations and functions. This protocol requires purified membrane protein in detergents, purified MSPs in solution, and detergent-destabilized phospholipids. The mixture of all three components at specific ratios is incubated in the presence of Bio-Beads SM-2 resins, which absorb all detergent molecules, allowing the membrane protein to associate with lipids surrounded by the MSPs. By reconstituting the purified membrane proteins back into their native-like lipid environment, these nanodisc-like particles can be directly used in cryo-EM single-particle analysis for structure determination and other biophysical analyses. It is noted that nanodiscs may potentially limit the dynamics of membrane proteins due to suboptimal nanodisc size compared to the native lipid bilayer. Key features • This protocol was built based on the method originally developed by Sligar et al. [1] and modified for a specific major facilitator superfamily transporter • This protocol is robust and reproducible • Lipid nanodiscs can increase membrane protein stability, and reconstituted transporters in lipid nanodiscs can regain function if their function is compromised using detergents • The reconstituted lipids nanodisc can be used for cryo-EM single-particle analysis.
Collapse
Affiliation(s)
- Parameswaran Hariharan
- Dept of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Lan Guan
- Dept of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| |
Collapse
|
2
|
Hariharan P, Shi Y, Katsube S, Willibal K, Burrows ND, Mitchell P, Bakhtiiari A, Stanfield S, Pardon E, Kaback HR, Liang R, Steyaert J, Viner R, Guan L. Mobile barrier mechanisms for Na +-coupled symport in an MFS sugar transporter. eLife 2024; 12:RP92462. [PMID: 38381130 PMCID: PMC10942615 DOI: 10.7554/elife.92462] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2024] Open
Abstract
While many 3D structures of cation-coupled transporters have been determined, the mechanistic details governing the obligatory coupling and functional regulations still remain elusive. The bacterial melibiose transporter (MelB) is a prototype of major facilitator superfamily transporters. With a conformation-selective nanobody, we determined a low-sugar affinity inward-facing Na+-bound cryoEM structure. The available outward-facing sugar-bound structures showed that the N- and C-terminal residues of the inner barrier contribute to the sugar selectivity. The inward-open conformation shows that the sugar selectivity pocket is also broken when the inner barrier is broken. Isothermal titration calorimetry measurements revealed that this inward-facing conformation trapped by this nanobody exhibited a greatly decreased sugar-binding affinity, suggesting the mechanisms for substrate intracellular release and accumulation. While the inner/outer barrier shift directly regulates the sugar-binding affinity, it has little or no effect on the cation binding, which is supported by molecular dynamics simulations. Furthermore, the hydron/deuterium exchange mass spectrometry analyses allowed us to identify dynamic regions; some regions are involved in the functionally important inner barrier-specific salt-bridge network, which indicates their critical roles in the barrier switching mechanisms for transport. These complementary results provided structural and dynamic insights into the mobile barrier mechanism for cation-coupled symport.
Collapse
Affiliation(s)
- Parameswaran Hariharan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, School of MedicineLubbockUnited States
| | - Yuqi Shi
- Thermo Fisher ScientificSan JoseUnited States
| | - Satoshi Katsube
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, School of MedicineLubbockUnited States
| | - Katleen Willibal
- VIB-VUB Center for Structural Biology, VIB, Pleinlaan 2BrusselsBelgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2BrusselsBelgium
| | - Nathan D Burrows
- Division of CryoEM and Bioimaging, Stanford Synchrotron Radiation Light Source, SLAC National Accelerator LaboratoryMenlo ParkUnited States
| | - Patrick Mitchell
- Division of CryoEM and Bioimaging, Stanford Synchrotron Radiation Light Source, SLAC National Accelerator LaboratoryMenlo ParkUnited States
| | | | - Samantha Stanfield
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, School of MedicineLubbockUnited States
| | - Els Pardon
- VIB-VUB Center for Structural Biology, VIB, Pleinlaan 2BrusselsBelgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2BrusselsBelgium
| | - H Ronald Kaback
- Department of Physiology, University of California, Los AngelesLos AngelesUnited States
| | - Ruibin Liang
- Department of Chemistry and Biochemistry, Texas Tech UniversityLubbockUnited States
| | - Jan Steyaert
- VIB-VUB Center for Structural Biology, VIB, Pleinlaan 2BrusselsBelgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2BrusselsBelgium
| | - Rosa Viner
- Thermo Fisher ScientificSan JoseUnited States
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, School of MedicineLubbockUnited States
| |
Collapse
|
3
|
Drew D, Boudker O. Ion and lipid orchestration of secondary active transport. Nature 2024; 626:963-974. [PMID: 38418916 DOI: 10.1038/s41586-024-07062-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 01/12/2024] [Indexed: 03/02/2024]
Abstract
Transporting small molecules across cell membranes is an essential process in cell physiology. Many structurally diverse, secondary active transporters harness transmembrane electrochemical gradients of ions to power the uptake or efflux of nutrients, signalling molecules, drugs and other ions across cell membranes. Transporters reside in lipid bilayers on the interface between two aqueous compartments, where they are energized and regulated by symported, antiported and allosteric ions on both sides of the membrane and the membrane bilayer itself. Here we outline the mechanisms by which transporters couple ion and solute fluxes and discuss how structural and mechanistic variations enable them to meet specific physiological needs and adapt to environmental conditions. We then consider how general bilayer properties and specific lipid binding modulate transporter activity. Together, ion gradients and lipid properties ensure the effective transport, regulation and distribution of small molecules across cell membranes.
Collapse
Affiliation(s)
- David Drew
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
| | - Olga Boudker
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
- Howard Hughes Medical Institute, Weill Cornell Medicine, New York, NY, USA.
| |
Collapse
|
4
|
Hariharan P, Shi Y, Katsube S, Willibal K, Burrows ND, Mitchell P, Bakhtiiari A, Stanfield S, Pardon E, Kaback HR, Liang R, Steyaert J, Viner R, Guan L. Mobile barrier mechanisms for Na +-coupled symport in an MFS sugar transporter. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.18.558283. [PMID: 37790566 PMCID: PMC10542114 DOI: 10.1101/2023.09.18.558283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
While many 3D structures of cation-coupled transporters have been determined, the mechanistic details governing the obligatory coupling and functional regulations still remain elusive. The bacterial melibiose transporter (MelB) is a prototype of the Na+-coupled major facilitator superfamily transporters. With a conformational nanobody (Nb), we determined a low-sugar affinity inward-facing Na+-bound cryoEM structure. Collectively with the available outward-facing sugar-bound structures, both the outer and inner barriers were localized. The N- and C-terminal residues of the inner barrier contribute to the sugar selectivity pocket. When the inner barrier is broken as shown in the inward-open conformation, the sugar selectivity pocket is also broken. The binding assays by isothermal titration calorimetry revealed that this inward-facing conformation trapped by the conformation-selective Nb exhibited a greatly decreased sugar-binding affinity, suggesting the mechanisms for the substrate intracellular release and accumulation. While the inner/outer barrier shift directly regulates the sugar-binding affinity, it has little or no effect on the cation binding, which is also supported by molecular dynamics simulations. Furthermore, the use of this Nb in combination with the hydron/deuterium exchange mass spectrometry allowed us to identify dynamic regions; some regions are involved in the functionally important inner barrier-specific salt-bridge network, which indicates their critical roles in the barrier switching mechanisms for transport. These complementary results provided structural and dynamic insights into the mobile barrier mechanism for cation-coupled symport.
Collapse
Affiliation(s)
- Parameswaran Hariharan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, School of Medicine, Lubbock, TX 79424, USA
| | - Yuqi Shi
- Thermo Fisher Scientific, San Jose, CA 95134, USA
| | - Satoshi Katsube
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, School of Medicine, Lubbock, TX 79424, USA
| | | | - Nathan D. Burrows
- Division of CryoEM and Bioimaging, Stanford Synchrotron Radiation Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Patrick Mitchell
- Division of CryoEM and Bioimaging, Stanford Synchrotron Radiation Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | | | - Samantha Stanfield
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, School of Medicine, Lubbock, TX 79424, USA
| | - Els Pardon
- VIB-VUB Center for Structural Biology, 1050 Brussel, Belgium
| | - H. Ronald Kaback
- Department of Physiology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ruibin Liang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Jan Steyaert
- VIB-VUB Center for Structural Biology, 1050 Brussel, Belgium
| | - Rosa Viner
- Thermo Fisher Scientific, San Jose, CA 95134, USA
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, School of Medicine, Lubbock, TX 79424, USA
| |
Collapse
|
5
|
Blaimschein N, Parameswaran H, Nagler G, Manioglu S, Helenius J, Ardelean C, Kuhn A, Guan L, Müller DJ. The insertase YidC chaperones the polytopic membrane protein MelB inserting and folding simultaneously from both termini. Structure 2023; 31:1419-1430.e5. [PMID: 37708891 PMCID: PMC10840855 DOI: 10.1016/j.str.2023.08.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/22/2023] [Accepted: 08/18/2023] [Indexed: 09/16/2023]
Abstract
The insertion and folding of proteins into membranes is crucial for cell viability. Yet, the detailed contributions of insertases remain elusive. Here, we monitor how the insertase YidC guides the folding of the polytopic melibiose permease MelB into membranes. In vivo experiments using conditionally depleted E. coli strains show that MelB can insert in the absence of SecYEG if YidC resides in the cytoplasmic membrane. In vitro single-molecule force spectroscopy reveals that the MelB substrate itself forms two folding cores from which structural segments insert stepwise into the membrane. However, misfolding dominates, particularly in structural regions that interface the pseudo-symmetric α-helical domains of MelB. Here, YidC takes an important role in accelerating and chaperoning the stepwise insertion and folding process of both MelB folding cores. Our findings reveal a great flexibility of the chaperoning and insertase activity of YidC in the multifaceted folding processes of complex polytopic membrane proteins.
Collapse
Affiliation(s)
- Nina Blaimschein
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, 4058 Basel, Basel-Stadt, Switzerland
| | - Hariharan Parameswaran
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Gisela Nagler
- Institute of Biology, University of Hohenheim, 70599 Stuttgart, Baden-Württemberg, Germany
| | - Selen Manioglu
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, 4058 Basel, Basel-Stadt, Switzerland
| | - Jonne Helenius
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, 4058 Basel, Basel-Stadt, Switzerland
| | | | - Andreas Kuhn
- Institute of Biology, University of Hohenheim, 70599 Stuttgart, Baden-Württemberg, Germany
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Daniel J Müller
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, 4058 Basel, Basel-Stadt, Switzerland.
| |
Collapse
|
6
|
Tang H, Li H, Prakaash D, Pedebos C, Qiu X, Sauer DB, Khalid S, Duerr K, Robinson CV. The solute carrier SPNS2 recruits PI(4,5)P 2 to synergistically regulate transport of sphingosine-1-phosphate. Mol Cell 2023; 83:2739-2752.e5. [PMID: 37499662 PMCID: PMC10790328 DOI: 10.1016/j.molcel.2023.06.033] [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: 11/30/2022] [Revised: 05/11/2023] [Accepted: 06/26/2023] [Indexed: 07/29/2023]
Abstract
Solute carrier spinster homolog 2 (SPNS2), one of only four known major facilitator superfamily (MFS) lysolipid transporters in humans, exports sphingosine-1-phosphate (S1P) across cell membranes. Here, we explore the synergistic effects of lipid binding and conformational dynamics on SPNS2's transport mechanism. Using mass spectrometry, we discovered that SPNS2 interacts preferentially with PI(4,5)P2. Together with functional studies and molecular dynamics (MD) simulations, we identified potential PI(4,5)P2 binding sites. Mutagenesis of proposed lipid binding sites and inhibition of PI(4,5)P2 synthesis reduce S1P transport, whereas the absence of the N terminus renders the transporter essentially inactive. Probing the conformational dynamics of SPNS2, we show how synergistic binding of PI(4,5)P2 and S1P facilitates transport, increases dynamics of the extracellular gate, and stabilizes the intracellular gate. Given that SPNS2 transports a key signaling lipid, our results have implications for therapeutic targeting and also illustrate a regulatory mechanism for MFS transporters.
Collapse
Affiliation(s)
- Haiping Tang
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK; Kavli Institute for Nanoscience Discovery, Oxford OX1 3QU, UK
| | - Huanyu Li
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Dheeraj Prakaash
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Conrado Pedebos
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Xingyu Qiu
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK; Kavli Institute for Nanoscience Discovery, Oxford OX1 3QU, UK
| | - David B Sauer
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Syma Khalid
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Katharina Duerr
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK; OMass Therapeutics, Ltd., Oxford OX4 2GX, UK
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK; Kavli Institute for Nanoscience Discovery, Oxford OX1 3QU, UK.
| |
Collapse
|
7
|
Katsube S, Willibal K, Vemulapally S, Hariharan P, Tikhonova E, Pardon E, Kaback HR, Steyaert J, Guan L. In vivo and in vitro characterizations of melibiose permease (MelB) conformation-dependent nanobodies reveal sugar-binding mechanisms. J Biol Chem 2023; 299:104967. [PMID: 37380079 PMCID: PMC10374971 DOI: 10.1016/j.jbc.2023.104967] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 06/13/2023] [Accepted: 06/19/2023] [Indexed: 06/30/2023] Open
Abstract
Salmonella enterica serovar Typhimurium melibiose permease (MelBSt) is a prototype of the Na+-coupled major facilitator superfamily transporters, which are important for the cellular uptake of molecules including sugars and small drugs. Although the symport mechanisms have been well-studied, mechanisms of substrate binding and translocation remain enigmatic. We have previously determined the sugar-binding site of outward-facing MelBSt by crystallography. To obtain other key kinetic states, here we raised camelid single-domain nanobodies (Nbs) and carried out a screening against the WT MelBSt under 4 ligand conditions. We applied an in vivo cAMP-dependent two-hybrid assay to detect interactions of Nbs with MelBSt and melibiose transport assays to determine the effects on MelBSt functions. We found that all selected Nbs showed partial to complete inhibitions of MelBSt transport activities, confirming their intracellular interactions. A group of Nbs (714, 725, and 733) was purified, and isothermal titration calorimetry measurements showed that their binding affinities were significantly inhibited by the substrate melibiose. When titrating melibiose to the MelBSt/Nb complexes, Nb also inhibited the sugar-binding. However, the Nb733/MelBSt complex retained binding to the coupling cation Na+ and also to the regulatory enzyme EIIAGlc of the glucose-specific phosphoenolpyruvate/sugar phosphotransferase system. Further, EIIAGlc/MelBSt complex also retained binding to Nb733 and formed a stable supercomplex. All data indicated that MelBSt trapped by Nbs retained its physiological functions and the trapped conformation is similar to that bound by the physiological regulator EIIAGlc. Therefore, these conformational Nbs can be useful tools for further structural, functional, and conformational analyses.
Collapse
Affiliation(s)
- Satoshi Katsube
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas, USA
| | - Katleen Willibal
- VIB Center for Structural Biology Research, VIB, Brussel, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, Brussel, Belgium
| | - Sangama Vemulapally
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas, USA
| | - Parameswaran Hariharan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas, USA
| | - Elena Tikhonova
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas, USA
| | - Els Pardon
- VIB Center for Structural Biology Research, VIB, Brussel, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, Brussel, Belgium
| | - H Ronald Kaback
- Department of Physiology and Department of Microbiology, Immunology, and Molecular Genetics, Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California, USA
| | - Jan Steyaert
- VIB Center for Structural Biology Research, VIB, Brussel, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, Brussel, Belgium
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas, USA.
| |
Collapse
|
8
|
Panda A, Giska F, Duncan AL, Welch AJ, Brown C, McAllister R, Hariharan P, Goder JND, Coleman J, Ramakrishnan S, Pincet F, Guan L, Krishnakumar S, Rothman JE, Gupta K. Direct determination of oligomeric organization of integral membrane proteins and lipids from intact customizable bilayer. Nat Methods 2023; 20:891-897. [PMID: 37106230 PMCID: PMC10932606 DOI: 10.1038/s41592-023-01864-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 03/23/2023] [Indexed: 04/29/2023]
Abstract
Hierarchical organization of integral membrane proteins (IMP) and lipids at the membrane is essential for regulating myriad downstream signaling. A quantitative understanding of these processes requires both detections of oligomeric organization of IMPs and lipids directly from intact membranes and determination of key membrane components and properties that regulate them. Addressing this, we have developed a platform that enables native mass spectrometry (nMS) analysis of IMP-lipid complexes directly from intact and customizable lipid membranes. Both the lipid composition and membrane properties (such as curvature, tension, and fluidity) of these bilayers can be precisely customized to a target membrane. Subsequent direct nMS analysis of these intact proteolipid vesicles can yield the oligomeric states of the embedded IMPs, identify bound lipids, and determine the membrane properties that can regulate the observed IMP-lipid organization. Applying this method, we show how lipid binding regulates neurotransmitter release and how membrane composition regulates the functional oligomeric state of a transporter.
Collapse
Affiliation(s)
- Aniruddha Panda
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Fabian Giska
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Anna L Duncan
- Department of Biochemistry, University of Oxford, Oxford, UK
- Department of Chemistry, Aarhus University, Aarhus C, Denmark
| | | | - Caroline Brown
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Rachel McAllister
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Parameswaran Hariharan
- Department of Cell Physiology and Molecular Biophysics, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Jean N D Goder
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Jeff Coleman
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Sathish Ramakrishnan
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Frédéric Pincet
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Laboratoire de Physique de l'Ecole Normale Supérieure, ENS, CNRS, Université PSL, Sorbonne Université, Université Paris-Cité, Paris, France
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Shyam Krishnakumar
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Neurology, Yale University School of Medicine, New Haven, CT, USA
| | - James E Rothman
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Kallol Gupta
- Nanobiology Institute, Yale University, West Haven, CT, USA.
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA.
| |
Collapse
|
9
|
Moreno-Cabezuelo JÁ, Del Carmen Muñoz-Marín M, López-Lozano A, Athayde D, Simón-García A, Díez J, Archer M, Issoglio FM, García-Fernández JM. Production, homology modeling and mutagenesis studies on GlcH glucose transporter from Prochlorococcus sp. strain SS120. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2023; 1864:148954. [PMID: 36563737 DOI: 10.1016/j.bbabio.2022.148954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 12/13/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022]
Abstract
The marine cyanobacterium Prochlorococcus is one of the main primary producers on Earth, which can take up glucose by using the high affinity, multiphasic transporter GlcH. We report here the overexpression of glcH from Prochlorococcus marinus strain SS120 in Escherichia coli. Modeling studies of GlcH using the homologous MelB melibiose transporter from Salmonella enterica serovar Typhimurium showed high conservation at the overall fold. We observed that an important structural interaction, mediated by a strong hydrogen bond between D8 and R141, is conserved in Prochlorococcus, although the corresponding amino acids in MelB from Salmonella are different. Biased docking studies suggested that when glucose reaches the pocket of the transporter and interacts with D8 and R141, the hydrogen bond network in which these residues are involved could be disrupted, favoring a conformational change with the subsequent translocation of the glucose molecule towards the cytoplasmic region of the pmGlcH structure. Based on these theoretical predictions and on the conservation of N117 and W348 in other MelB structures, D8, N117, R141 and W348 were mutated to glycine residues. Their key role in glucose transport was evaluated by glucose uptake assays. N117G and W348G mutations led to 17 % decrease in glucose uptake, while D8G and R141G decreased the glucose transport by 66 % and 92 % respectively. Overall, our studies provide insights into the Prochlorococcus 3D-structure of GlcH, paving the way for further analysis to understand the features which are involved in the high affinity and multiphasic kinetics of this transporter.
Collapse
Affiliation(s)
- José Ángel Moreno-Cabezuelo
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
| | - María Del Carmen Muñoz-Marín
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
| | - Antonio López-Lozano
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
| | - Diogo Athayde
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157 Oeiras, Portugal
| | - Ana Simón-García
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
| | - Jesús Díez
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
| | - Margarida Archer
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157 Oeiras, Portugal
| | - Federico M Issoglio
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157 Oeiras, Portugal; CONICET-Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Buenos Aires, Argentina.
| | - José Manuel García-Fernández
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain.
| |
Collapse
|
10
|
Li Y, Ge X. Role of Berberine as a Potential Efflux Pump Inhibitor against MdfA from Escherichia coli: In Vitro and In Silico Studies. Microbiol Spectr 2023; 11:e0332422. [PMID: 36786641 PMCID: PMC10100983 DOI: 10.1128/spectrum.03324-22] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 01/30/2023] [Indexed: 02/15/2023] Open
Abstract
Infections by Gram-negative pathogens are usually difficult to manage due to the drug export by efflux pumps. With the evolution and horizontal transfer of efflux pumps, there is an urgent need to discover safe and effective efflux pump inhibitors. Here, we found that the natural compound berberine (BBR), a traditional medicine for intestinal infection, is an inhibitor against the major facilitator superfamily (MFS) efflux pump MdfA in Escherichia coli. The impact of BBR on MdfA was evaluated in a recombinant E. coli reporter strain. We demonstrated that low levels of BBR significantly increased intracellular ciprofloxacin concentrations and restored antibiotic susceptibility of the reporter strain. At the same time, we conducted molecular dynamics simulations to investigate the mechanisms of BBR's effect on MdfA. Our data indicated that BBR can aggregate to the periplasmic and cytoplasmic sides of MdfA in both of its inward and outward conformations. Protein rigidities were affected to different degrees. More importantly, two major driving forces for the conformational transition, salt bridges and hydrophilic interactions with water, were changed by BBR's aggregation to MdfA, which affected its conformational transition. In summary, our data provide evidence for the extended application of BBR as an efflux pump inhibitor at a clinically meaningful level. We also reveal the mechanisms and provide insights into BBR's effect on the reciprocal motion of MdfA. IMPORTANCE In this work, we evaluated the role of berberine (BBR) as an inhibitor of the MFS efflux pump MdfA from E. coli. We demonstrated that low levels of BBR significantly increased intracellular ciprofloxacin concentrations and restored antibiotic susceptibility of the reporter strain. Molecular dynamics simulations revealed the effect of BBR on the conformational transition of MdfA. Our data suggested that driving forces for MdfA's conformational transition were affected by BBR and provided evidence for BBR's extended application as an effective inhibitor of MdfA.
Collapse
Affiliation(s)
- Ying Li
- College of Biochemical Engineering, Beijing Union University, Beijing, China
| | - Xizhen Ge
- College of Biochemical Engineering, Beijing Union University, Beijing, China
| |
Collapse
|
11
|
Blaimschein N, Hariharan P, Manioglu S, Guan L, Müller DJ. Substrate-binding guides individual melibiose permeases MelB to structurally soften and to destabilize cytoplasmic middle-loop C3. Structure 2023; 31:58-67.e4. [PMID: 36525976 PMCID: PMC9825662 DOI: 10.1016/j.str.2022.11.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 11/06/2022] [Accepted: 11/18/2022] [Indexed: 12/23/2022]
Abstract
The melibiose permease MelB is a well-studied Na+-coupled transporter of the major facilitator superfamily. However, the symport mechanism of galactosides and cations is still not fully understood, especially at structural levels. Here, we use single-molecule force spectroscopy to investigate substrate-induced structural changes of MelB from Salmonella typhimurium. In the absence of substrate, MelB equally populates two different states, from which one shows higher mechanical structural stability with additional stabilization of the cytoplasmic middle-loop C3. In the presence of either melibiose or a coupling Na+-cation, however, MelB increasingly populates the mechanically less stable state, which shows a destabilized middle-loop C3. In the presence of both substrate and co-substrate, this mechanically less stable state of MelB is predominant. Our findings describe how both substrates guide MelB transporters to populate two different mechanically stabilized states, and contribute mechanistic insights to the alternating-access action for the galactoside/cation symport catalyzed by MelB.
Collapse
Affiliation(s)
- Nina Blaimschein
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, 4058 Basel, Switzerland
| | - Parameswaran Hariharan
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Selen Manioglu
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, 4058 Basel, Switzerland
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA.
| | - Daniel J Müller
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, 4058 Basel, Switzerland.
| |
Collapse
|
12
|
van Beekveld RAM, Derks MGN, Kumar R, Smid L, Maass T, Medeiros‐Silva J, Breukink E, Weingarth M. Specific Lipid Studies in Complex Membranes by Solid-State NMR Spectroscopy. Chemistry 2022; 28:e202202472. [PMID: 36098094 PMCID: PMC10092488 DOI: 10.1002/chem.202202472] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Indexed: 11/11/2022]
Abstract
Specific interactions with phospholipids are often critical for the function of proteins or drugs, but studying these interactions at high resolution remains difficult, especially in complex membranes that mimic biological conditions. In principle, molecular interactions with phospholipids could be directly probed by solid-state NMR (ssNMR). However, due to the challenge to detect specific lipids in mixed liposomes and limited spectral sensitivity, ssNMR studies of specific lipids in complex membranes are scarce. Here, by using purified biological 13 C,15 N-labeled phospholipids, we show that we can selectively detect traces of specific lipids in complex membranes. In combination with 1 H-detected ssNMR, we show that our approach provides unprecedented high-resolution insights into the mechanisms of drugs that target specific lipids. This broadly applicable approach opens new opportunities for the molecular characterization of specific lipid interactions with proteins or drugs in complex fluid membranes.
Collapse
Affiliation(s)
- Roy A. M. van Beekveld
- NMR SpectroscopyDepartment of ChemistryFaculty of ScienceUtrecht UniversityPadualaan 83584 CHUtrechtThe Netherlands
| | - Maik G. N. Derks
- NMR SpectroscopyDepartment of ChemistryFaculty of ScienceUtrecht UniversityPadualaan 83584 CHUtrechtThe Netherlands
- Membrane Biochemistry and BiophysicsDepartment of ChemistryFaculty of ScienceUtrecht UniversityPadualaan 83584 CHUtrechtThe Netherlands
| | - Raj Kumar
- NMR SpectroscopyDepartment of ChemistryFaculty of ScienceUtrecht UniversityPadualaan 83584 CHUtrechtThe Netherlands
| | - Leanna Smid
- NMR SpectroscopyDepartment of ChemistryFaculty of ScienceUtrecht UniversityPadualaan 83584 CHUtrechtThe Netherlands
| | - Thorben Maass
- NMR SpectroscopyDepartment of ChemistryFaculty of ScienceUtrecht UniversityPadualaan 83584 CHUtrechtThe Netherlands
| | - João Medeiros‐Silva
- NMR SpectroscopyDepartment of ChemistryFaculty of ScienceUtrecht UniversityPadualaan 83584 CHUtrechtThe Netherlands
- Present address: Department of ChemistryMassachusetts Institute of Technology170 Albany StreetCambridgeMA 02139USA
| | - Eefjan Breukink
- Membrane Biochemistry and BiophysicsDepartment of ChemistryFaculty of ScienceUtrecht UniversityPadualaan 83584 CHUtrechtThe Netherlands
| | - Markus Weingarth
- NMR SpectroscopyDepartment of ChemistryFaculty of ScienceUtrecht UniversityPadualaan 83584 CHUtrechtThe Netherlands
| |
Collapse
|
13
|
Li Y, Ge X. Discovering interrelated natural mutations of efflux pump KmrA from Klebsiella pneumoniae that confer increased multidrug resistance. Protein Sci 2022; 31:e4323. [PMID: 35634772 PMCID: PMC9083138 DOI: 10.1002/pro.4323] [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: 12/30/2021] [Revised: 03/03/2022] [Accepted: 04/11/2022] [Indexed: 11/12/2022]
Abstract
Klebsiella pneumoniae is a notorious pathogen that can cause multiorgan infections, which is difficult to treat mainly due to the widely distributed efflux pumps. Our previous research discovered the upregulation of efflux pump KmrA conferred enhanced antibiotic resistance, while the export mechanism and its natural mutations across K. pneumoniae isolates remain unclear. Herein, we analyzed the natural mutations of KmrA across 830 K. pneumoniae genomes to discover interrelated amino-acid substitutions (simultaneously occurred substitutions) that increase drug export. We identified two variants that contain triple amino-acid substitutions near the periplasmic side and then confirmed their roles in enhancing multidrug resistance of recombinant K. pneumoniae strains. Molecular dynamics simulations were conducted to illustrate the reason for their promoted export efficiencies. Our data indicated the triple substitutions resulted in KmrA's both stronger hydrophilic interaction with water and hydrophobic interaction with membrane. Moreover, these substitutions promoted the flexibilities of KmrA that could facilitate the conformational switch. In parallel, stronger ionic interactions (salt bridges) at cytoplasmic side also suggested the higher possibilities for the reciprocal movements. Collectively we demonstrated the potential risk of the interrelated natural mutations in efflux pump to antibiotic resistance of K. pneumoniae and provided insights into the mechanism of the enhanced drug export.
Collapse
Affiliation(s)
- Ying Li
- College of Biochemical EngineeringBeijing Union UniversityBeijingChina
| | - Xizhen Ge
- College of Biochemical EngineeringBeijing Union UniversityBeijingChina
| |
Collapse
|
14
|
Li Y, Wen H, Ge X. Opposite motion of the Central Helices of efflux pump KmrA is important for its export efficiency. Microb Pathog 2022; 167:105570. [PMID: 35550844 DOI: 10.1016/j.micpath.2022.105570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 04/11/2022] [Accepted: 05/05/2022] [Indexed: 10/18/2022]
Abstract
Efflux pump of Major Facilitator Superfamily (MFS) is widely distributed in bacteria, while its role in regulating antibiotic resistance of nosocomial pathogen Klebsiella pneumoniae remains unclear. Herein we analyzed the effect of amino acid substitution of MFS efflux pump KmrA on its export efficiency via molecular biology and molecular dynamics (MD). After searching across the 804 sequenced K. pneumoniae isolates, we identified four major variants of KmrA, while one of them KmrA-A was demonstrated an inactive one in MIC and ethidium bromide efflux assays. Subsequently, MD simulations of KmrA and its variants were conducted and the opposite motion of the central helices were observed for the active variants, while it was not found for KmrA-A. To further identify the importance of the opposite motion to the conformational transition, we calculated their differences in volume of binding pocket, salt bridge and hydrophilic interaction with water based on the rocker-switch model. Our results indicated that the opposite motion of KmrA conferred a larger binding pocket and stronger hydrogen bond with water at inward-facing conformation. An unusual substitution S374A of KmrA-A disrupted the normal motion of central helices by enhancing hydrophobic interactions between them, resulting into the altered positions and strengths of salt bridge, which was deduced to affect the conformational transition. Overall our data provided detailed information on the regular of KmrA's moving trajectory, demonstrating the importance of opposite motion of central helices to KmrA's export efficiency.
Collapse
Affiliation(s)
- Ying Li
- College of Biochemical Engineering, Beijing Union University, Beijing, 100023, China
| | - Honglin Wen
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, 100010, China
| | - Xizhen Ge
- College of Biochemical Engineering, Beijing Union University, Beijing, 100023, China.
| |
Collapse
|
15
|
Katsube S, Liang R, Amin A, Hariharan P, Guan L. Molecular basis for the cation selectivity of Salmonella typhimurium melibiose permease. J Mol Biol 2022; 434:167598. [DOI: 10.1016/j.jmb.2022.167598] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/14/2022] [Accepted: 04/14/2022] [Indexed: 12/23/2022]
|
16
|
Bacle A, Buslaev P, Garcia-Fandino R, Favela-Rosales F, Mendes Ferreira T, Fuchs PFJ, Gushchin I, Javanainen M, Kiirikki AM, Madsen JJ, Melcr J, Milán Rodríguez P, Miettinen MS, Ollila OHS, Papadopoulos CG, Peón A, Piggot TJ, Piñeiro Á, Virtanen SI. Inverse Conformational Selection in Lipid-Protein Binding. J Am Chem Soc 2021; 143:13701-13709. [PMID: 34465095 DOI: 10.1021/jacs.1c05549] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Interest in lipid interactions with proteins and other biomolecules is emerging not only in fundamental biochemistry but also in the field of nanobiotechnology where lipids are commonly used, for example, in carriers of mRNA vaccines. The outward-facing components of cellular membranes and lipid nanoparticles, the lipid headgroups, regulate membrane interactions with approaching substances, such as proteins, drugs, RNA, or viruses. Because lipid headgroup conformational ensembles have not been experimentally determined in physiologically relevant conditions, an essential question about their interactions with other biomolecules remains unanswered: Do headgroups exchange between a few rigid structures, or fluctuate freely across a practically continuous spectrum of conformations? Here, we combine solid-state NMR experiments and molecular dynamics simulations from the NMRlipids Project to resolve the conformational ensembles of headgroups of four key lipid types in various biologically relevant conditions. We find that lipid headgroups sample a wide range of overlapping conformations in both neutral and charged cellular membranes, and that differences in the headgroup chemistry manifest only in probability distributions of conformations. Furthermore, the analysis of 894 protein-bound lipid structures from the Protein Data Bank suggests that lipids can bind to proteins in a wide range of conformations, which are not limited by the headgroup chemistry. We propose that lipids can select a suitable headgroup conformation from the wide range available to them to fit the various binding sites in proteins. The proposed inverse conformational selection model will extend also to lipid binding to targets other than proteins, such as drugs, RNA, and viruses.
Collapse
Affiliation(s)
- Amélie Bacle
- Laboratoire Coopératif "Lipotoxicity and Channelopathies - ConicMeds", Université de Poitiers, 1 rue Georges Bonnet, Poitiers 86000, France
| | - Pavel Buslaev
- Nanoscience Center and Department of Chemistry, University of Jyväskylä, P.O. Box 35, Jyväskylä 40014, Finland.,Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Rebeca Garcia-Fandino
- Center for Research in Biological Chemistry and Molecular Materials (CiQUS), Universidade de Santiago de Compostela, Santiago de Compostela E-15782, Spain.,CIQUP, Centro de Investigao em Química, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto 4169-007, Portugal
| | - Fernando Favela-Rosales
- Departamento de Ciencias Básicas, Tecnológico Nacional de México - ITS Zacatecas Occidente, Sombrerete, Zacatecas 99102, México
| | - Tiago Mendes Ferreira
- NMR group - Institute for Physics, Martin Luther University Halle-Wittenberg, Halle (Saale), 06120, Germany
| | - Patrick F J Fuchs
- Ecole Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules (LBM), Sorbonne Université, Paris 75005, France.,UFR Sciences du Vivant, Université de Paris, Paris 75013, France
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Matti Javanainen
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 542/2, Prague CZ-16610, Czech Republic
| | - Anne M Kiirikki
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - Jesper J Madsen
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States.,Global and Planetary Health, College of Public Health, University of South Florida, Tampa, Florida 33612, United States
| | - Josef Melcr
- Groningen Biomolecular Sciences and Biotechnology Institute and The Zernike Institute for Advanced Materials, University of Groningen, Groningen9747 AG, The Netherlands
| | - Paula Milán Rodríguez
- Ecole Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules (LBM), Sorbonne Université, Paris 75005, France
| | - Markus S Miettinen
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Potsdam 14424, Germany
| | - O H Samuli Ollila
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - Chris G Papadopoulos
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Gif-sur-Yvette 91198, France
| | - Antonio Peón
- CIQUP, Centro de Investigao em Química, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto 4169-007, Portugal
| | - Thomas J Piggot
- Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Ángel Piñeiro
- Departamento de Física Aplicada, Facultade de Física, Universidade de Santiago de Compostela, Santiago de Compostela E-15782, Spain
| | - Salla I Virtanen
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| |
Collapse
|
17
|
Markham KJ, Tikhonova EB, Scarpa AC, Hariharan P, Katsube S, Guan L. Complete cysteine-scanning mutagenesis of the Salmonella typhimurium melibiose permease. J Biol Chem 2021; 297:101090. [PMID: 34416232 PMCID: PMC8437787 DOI: 10.1016/j.jbc.2021.101090] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 08/10/2021] [Accepted: 08/16/2021] [Indexed: 11/15/2022] Open
Abstract
The melibiose permease of Salmonella typhimurium (MelBSt) catalyzes the stoichiometric symport of galactopyranoside with a cation (H+, Li+, or Na+) and is a prototype for Na+-coupled major facilitator superfamily (MFS) transporters presenting from bacteria to mammals. X-ray crystal structures of MelBSt have revealed the molecular recognition mechanism for sugar binding; however, understanding of the cation site and symport mechanism is still vague. To further investigate the transport mechanism and conformational dynamics of MelBSt, we generated a complete single-Cys library containing 476 unique mutants by placing a Cys at each position on a functional Cys-less background. Surprisingly, 105 mutants (22%) exhibit poor transport activities (<15% of Cys-less transport), although the expression levels of most mutants were comparable to that of the control. The affected positions are distributed throughout the protein. Helices I and X and transmembrane residues Asp and Tyr are most affected by cysteine replacement, while helix IX, the cytoplasmic middle-loop, and C-terminal tail are least affected. Single-Cys replacements at the major sugar-binding positions (K18, D19, D124, W128, R149, and W342) or at positions important for cation binding (D55, N58, D59, and T121) abolished the Na+-coupled active transport, as expected. We mapped 50 loss-of-function mutants outside of these substrate-binding sites that suffered from defects in protein expression/stability or conformational dynamics. This complete Cys-scanning mutagenesis study indicates that MelBSt is highly susceptible to single-Cys mutations, and this library will be a useful tool for further structural and functional studies to gain insights into the cation-coupled symport mechanism for Na+-coupled MFS transporters.
Collapse
Affiliation(s)
- Kelsey J Markham
- Department of Cell Physiology & Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, School of Medicine, Lubbock, Texas, USA
| | - Elena B Tikhonova
- Department of Cell Physiology & Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, School of Medicine, Lubbock, Texas, USA
| | - Aaron C Scarpa
- Department of Cell Physiology & Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, School of Medicine, Lubbock, Texas, USA
| | - Parameswaran Hariharan
- Department of Cell Physiology & Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, School of Medicine, Lubbock, Texas, USA
| | - Satoshi Katsube
- Department of Cell Physiology & Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, School of Medicine, Lubbock, Texas, USA
| | - Lan Guan
- Department of Cell Physiology & Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, School of Medicine, Lubbock, Texas, USA.
| |
Collapse
|
18
|
Guan L, Hariharan P. X-ray crystallography reveals molecular recognition mechanism for sugar binding in a melibiose transporter MelB. Commun Biol 2021; 4:931. [PMID: 34341464 PMCID: PMC8329300 DOI: 10.1038/s42003-021-02462-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 07/07/2021] [Indexed: 12/15/2022] Open
Abstract
Major facilitator superfamily_2 transporters are widely found from bacteria to mammals. The melibiose transporter MelB, which catalyzes melibiose symport with either Na+, Li+, or H+, is a prototype of the Na+-coupled MFS transporters, but its sugar recognition mechanism has been a long-unsolved puzzle. Two high-resolution X-ray crystal structures of a Salmonella typhimurium MelB mutant with a bound ligand, either nitrophenyl-α-d-galactoside or dodecyl-β-d-melibioside, were refined to a resolution of 3.05 or 3.15 Å, respectively. In the substrate-binding site, the interaction of both galactosyl moieties on the two ligands with MelBSt are virturally same, so the sugar specificity determinant pocket can be recognized, and hence the molecular recognition mechanism for sugar binding in MelB has been deciphered. The conserved cation-binding pocket is also proposed, which directly connects to the sugar specificity pocket. These key structural findings have laid a solid foundation for our understanding of the cooperative binding and symport mechanisms in Na+-coupled MFS transporters, including eukaryotic transporters such as MFSD2A. Guan and Hariharan report two crystal structures of melibiose transporter MelB in complex with substrate analogs, nitrophenyl-galactoside, and dodecyl-melibioside. Both structures revealed similar specific site for sugar recognition and resolved the cation-binding pocket, advancing the understanding of MelB and related transporters.
Collapse
Affiliation(s)
- Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA.
| | - Parameswaran Hariharan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| |
Collapse
|
19
|
Jodaitis L, van Oene T, Martens C. Assessing the Role of Lipids in the Molecular Mechanism of Membrane Proteins. Int J Mol Sci 2021; 22:7267. [PMID: 34298884 PMCID: PMC8306737 DOI: 10.3390/ijms22147267] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/30/2021] [Accepted: 07/01/2021] [Indexed: 02/06/2023] Open
Abstract
Membrane proteins have evolved to work optimally within the complex environment of the biological membrane. Consequently, interactions with surrounding lipids are part of their molecular mechanism. Yet, the identification of lipid-protein interactions and the assessment of their molecular role is an experimental challenge. Recently, biophysical approaches have emerged that are compatible with the study of membrane proteins in an environment closer to the biological membrane. These novel approaches revealed specific mechanisms of regulation of membrane protein function. Lipids have been shown to play a role in oligomerization, conformational transitions or allosteric coupling. In this review, we summarize the recent biophysical approaches, or combination thereof, that allow to decipher the role of lipid-protein interactions in the mechanism of membrane proteins.
Collapse
Affiliation(s)
| | | | - Chloé Martens
- Center for Structural Biology and Bioinformatics, Université Libre de Bruxelles, 1050 Brussels, Belgium; (L.J.); (T.v.O.)
| |
Collapse
|
20
|
Hariharan P, Guan L. Cooperative binding ensures the obligatory melibiose/Na+ cotransport in MelB. J Gen Physiol 2021; 153:212278. [PMID: 34110360 PMCID: PMC8200842 DOI: 10.1085/jgp.202012710] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 04/07/2021] [Accepted: 05/14/2021] [Indexed: 11/20/2022] Open
Abstract
MelB catalyzes the obligatory cotransport of melibiose with Na+, Li+, or H+. Crystal structure determination of the Salmonella typhimurium MelB (MelBSt) has revealed a typical major facilitator superfamily (MFS) fold at a periplasmic open conformation. Cooperative binding of Na+ and melibiose has been previously established. To determine why cotranslocation of sugar solute and cation is obligatory, we analyzed each binding in the thermodynamic cycle using three independent methods, including the determination of melting temperature by circular dichroism spectroscopy, heat capacity change (ΔCp), and regulatory phosphotransferase EIIAGlc binding with isothermal titration calorimetry (ITC). We found that MelBSt thermostability is increased by either substrate (Na+ or melibiose) and observed a cooperative effect of both substrates. ITC measurements showed that either binary formation yields a positive sign in the ΔCp, suggesting MelBSt hydration and a likely widening of the periplasmic cavity. Conversely, formation of a ternary complex yields negative values in ΔCp, suggesting MelBSt dehydration and cavity closure. Lastly, we observed that EIIAGlc, which has been suggested to trap MelBSt at an outward-open state, readily binds to the MelBSt apo state at an affinity similar to MelBSt/Na+. However, it has a suboptimal binding to the ternary state, implying that MelBSt in the ternary complex may be conformationally distant from the EIIAGlc-preferred outward-facing conformation. Our results consistently support the notion that binding of one substrate (Na+ or melibiose) favors MelBSt at open states, whereas the cooperative binding of both substrates triggers the alternating-access process, thus suggesting this conformational regulation could ensure the obligatory cotransport.
Collapse
Affiliation(s)
- Parameswaran Hariharan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX
| |
Collapse
|
21
|
Roque-Borda CA, Silva HRL, Crusca Junior E, Serafim JA, Meneguin AB, Chorilli M, Macedo WC, Teixeira SR, Guastalli EAL, Soares NM, Blair JMA, Pikramenou Z, Vicente EF. Alginate-based microparticles coated with HPMCP/AS cellulose-derivatives enable the Ctx(Ile 21)-Ha antimicrobial peptide application as a feed additive. Int J Biol Macromol 2021; 183:1236-1247. [PMID: 33965488 DOI: 10.1016/j.ijbiomac.2021.05.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/26/2021] [Accepted: 05/02/2021] [Indexed: 12/20/2022]
Abstract
Microencapsulation is a potential biotechnological tool, which can overcome antimicrobial peptides (AMP) instabilities and reduce toxic side effects. Thus, this study evaluates the antibacterial activities of the Ctx(Ile21)-Ha AMP against multidrug-resistant (MDR) and non-resistant bacteria and develop and characterize peptide-loaded microparticles coated with the enteric polymers hydroxypropylmethylcellulose acetate succinate (HPMCAS) and hydroxypropylmethylcellulose phthalate (HPMCP). Ctx(Ile21)-Ha was obtained by solid phase peptide synthesis (SPPS) method, purified and characterized by HPLC and Mass Spectrometry. The peptide exhibited potent antibiotic activities against Salmonella enteritidis, Salmonella typhimurium, Pseudomonas aeruginosa (MDR), Acinetobacter baumannii (MDR), and Staphylococcus aureus (MDR). Ctx(Ile21)-Ha microencapsulation was performed by ionic gelation with high efficiency, maintaining the physical-chemical stability. Ctx(Ile21)-Ha coated-microparticles were characterized by DSC, TGA, FTIR-Raman, XRD and SEM. Hemolytic activity assay demonstrated that hemolysis was decreased up to 95% compared to single molecule. In addition, in vitro release control profile simulating different portions of gastrointestinal tract was performed and showed the microcapsules' ability to protect the peptide and release it in the intestine, aiming pathogen's location, mainly by Salmonella sp. Therefore, use of microencapsulated Ctx(Ile21)-Ha can be allowed as an antimicrobial controller in monogastric animal production as an oral feed additive (antimicrobial controller), being a valuable option for molecules with low therapeutic indexes or high hemolytic rates.
Collapse
Affiliation(s)
- Cesar Augusto Roque-Borda
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Jaboticabal, São Paulo CEP 14884-900, Brazil
| | - Hanyeny Raiely Leite Silva
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Jaboticabal, São Paulo CEP 14884-900, Brazil
| | - Edson Crusca Junior
- São Paulo State University (Unesp), Institute of Chemistry, Araraquara, São Paulo CEP 14800-900, Brazil
| | - Jéssica Aparecida Serafim
- São Paulo State University (Unesp), School of Sciences and Engineering, Tupã, São Paulo CEP 17602-496, Brazil
| | - Andréia Bagliotti Meneguin
- São Paulo State University (Unesp), School of Pharmaceutical Sciences, Araraquara, São Paulo CEP 14801-902, Brazil
| | - Marlus Chorilli
- São Paulo State University (Unesp), School of Pharmaceutical Sciences, Araraquara, São Paulo CEP 14801-902, Brazil
| | - Wagner Costa Macedo
- São Paulo State University (Unesp), School of Technology and Sciences, Presidente Prudente, São Paulo CEP 19060-900, Brazil
| | - Silvio Rainho Teixeira
- São Paulo State University (Unesp), School of Technology and Sciences, Presidente Prudente, São Paulo CEP 19060-900, Brazil
| | | | - Nilce Maria Soares
- Poultry Health Specialized Laboratory, Biological Institute, Bastos, São Paulo CEP 17690000, Brazil
| | - Jessica M A Blair
- Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | - Zoe Pikramenou
- School of Chemistry, University of Birmingham, Birmingham B15 2TT, UK
| | - Eduardo Festozo Vicente
- São Paulo State University (Unesp), School of Sciences and Engineering, Tupã, São Paulo CEP 17602-496, Brazil.
| |
Collapse
|
22
|
Drew D, North RA, Nagarathinam K, Tanabe M. Structures and General Transport Mechanisms by the Major Facilitator Superfamily (MFS). Chem Rev 2021; 121:5289-5335. [PMID: 33886296 PMCID: PMC8154325 DOI: 10.1021/acs.chemrev.0c00983] [Citation(s) in RCA: 168] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Indexed: 12/12/2022]
Abstract
The major facilitator superfamily (MFS) is the largest known superfamily of secondary active transporters. MFS transporters are responsible for transporting a broad spectrum of substrates, either down their concentration gradient or uphill using the energy stored in the electrochemical gradients. Over the last 10 years, more than a hundred different MFS transporter structures covering close to 40 members have provided an atomic framework for piecing together the molecular basis of their transport cycles. Here, we summarize the remarkable promiscuity of MFS members in terms of substrate recognition and proton coupling as well as the intricate gating mechanisms undergone in achieving substrate translocation. We outline studies that show how residues far from the substrate binding site can be just as important for fine-tuning substrate recognition and specificity as those residues directly coordinating the substrate, and how a number of MFS transporters have evolved to form unique complexes with chaperone and signaling functions. Through a deeper mechanistic description of glucose (GLUT) transporters and multidrug resistance (MDR) antiporters, we outline novel refinements to the rocker-switch alternating-access model, such as a latch mechanism for proton-coupled monosaccharide transport. We emphasize that a full understanding of transport requires an elucidation of MFS transporter dynamics, energy landscapes, and the determination of how rate transitions are modulated by lipids.
Collapse
Affiliation(s)
- David Drew
- Department
of Biochemistry and Biophysics, Stockholm
University, SE 106 91 Stockholm, Sweden
| | - Rachel A. North
- Department
of Biochemistry and Biophysics, Stockholm
University, SE 106 91 Stockholm, Sweden
| | - Kumar Nagarathinam
- Center
of Structural and Cell Biology in Medicine, Institute of Biochemistry, University of Lübeck, D-23538, Lübeck, Germany
| | - Mikio Tanabe
- Structural
Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Oho 1-1, Tsukuba, Ibaraki 305-0801, Japan
| |
Collapse
|
23
|
Dowhan W, Bogdanov M. Eugene P. Kennedy's Legacy: Defining Bacterial Phospholipid Pathways and Function. Front Mol Biosci 2021; 8:666203. [PMID: 33842554 PMCID: PMC8027125 DOI: 10.3389/fmolb.2021.666203] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 03/01/2021] [Indexed: 12/27/2022] Open
Abstract
In the 1950's and 1960's Eugene P. Kennedy laid out the blueprint for phospholipid biosynthesis in somatic cells and Escherichia coli, which have been coined the Kennedy Pathways for phospholipid biosynthesis. His research group continued to make seminal contributions in the area of phospholipids until his retirement in the early 1990's. During these years he mentored many young scientists that continued to build on his early discoveries and who also mentored additional scientists that continue to make important contributions in areas related to phospholipids and membrane biogenesis. This review will focus on the initial E. coli Kennedy Pathways and how his early contributions have laid the foundation for our current understanding of bacterial phospholipid genetics, biochemistry and function as carried on by his scientific progeny and others who have been inspired to study microbial phospholipids.
Collapse
Affiliation(s)
- William Dowhan
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, United States
| | - Mikhail Bogdanov
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, United States
| |
Collapse
|
24
|
Harris NJ, Pellowe GA, Booth PJ. Cell-free expression tools to study co-translational folding of alpha helical membrane transporters. Sci Rep 2020; 10:9125. [PMID: 32499529 PMCID: PMC7272624 DOI: 10.1038/s41598-020-66097-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 05/15/2020] [Indexed: 11/28/2022] Open
Abstract
Most helical membrane proteins fold co-translationally during unidirectional polypeptide elongation by the ribosome. Studies thus far, however, have largely focussed on refolding full-length proteins from artificially induced denatured states that are far removed from the natural co-translational process. Cell-free translation offers opportunities to remedy this deficit in folding studies and has previously been used for membrane proteins. We exploit this cell-free approach to develop tools to probe co-translational folding. We show that two transporters from the ubiquitous Major Facilitator Superfamily can successfully insert into a synthetic bilayer without the need for translocon insertase apparatus that is essential in vivo. We also assess the cooperativity of domain insertion, by expressing the individual transporter domains cell-free. Furthermore, we manipulate the cell-free reaction to pause and re-start protein synthesis at specific points in the protein sequence. We find that full-length protein can still be made when stalling after the first N terminal helix has inserted into the bilayer. However, stalling after the first three helices have exited the ribosome cannot be successfully recovered. These three helices cannot insert stably when ribosome-bound during co-translational folding, as they require insertion of downstream helices.
Collapse
Affiliation(s)
- Nicola J Harris
- King's College London, Department of Chemistry, Britannia House, 7 Trinity Street, London, SE1 1DB, UK
| | - Grant A Pellowe
- King's College London, Department of Chemistry, Britannia House, 7 Trinity Street, London, SE1 1DB, UK
| | - Paula J Booth
- King's College London, Department of Chemistry, Britannia House, 7 Trinity Street, London, SE1 1DB, UK.
| |
Collapse
|
25
|
Vitrac H, Mallampalli VKPS, Azinas S, Dowhan W. Structural and Functional Adaptability of Sucrose and Lactose Permeases from Escherichia coli to the Membrane Lipid Composition. Biochemistry 2020; 59:1854-1868. [PMID: 32363862 DOI: 10.1021/acs.biochem.0c00174] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The lipid environment in which membrane proteins are embedded can influence their structure and function. Lipid-protein interactions and lipid-induced conformational changes necessary for protein function remain intractable in vivo using high-resolution techniques. Using Escherichia coli strains in which the normal phospholipid composition can be altered or foreign lipids can be introduced, we established the importance of membrane lipid composition for the proper folding, assembly, and function of E. coli lactose (LacY) and sucrose (CscB) permeases. However, the molecular mechanism underlying the lipid dependence for active transport remains unknown. Herein, we demonstrate that the structure and function of CscB and LacY can be modulated by the composition of the lipid environment. Using a combination of assays (transport activity of the substrate, protein topology, folding, and assembly into the membrane), we found that alterations in the membrane lipid composition lead to lipid-dependent structural changes in CscB and LacY. These changes affect the orientation of residues involved in LacY proton translocation and impact the rates of protonation and deprotonation of E325 by affecting the arrangement of transmembrane domains in the vicinity of the R302-E325 charge pair. Furthermore, the structural changes caused by changes in membrane lipid composition can be altered by a single-point mutation, highlighting the adaptability of these transporters to their environment. Altogether, our results demonstrate that direct interactions between a protein and its lipid environment uniquely contribute to membrane protein organization and function. Because members of the major facilitator superfamily present with well-conserved functional architecture, we anticipate that our findings can be extrapolated to other membrane protein transporters.
Collapse
Affiliation(s)
- Heidi Vitrac
- Department of Biochemistry and Molecular Biology and Center for Membrane Biology, University of Texas McGovern Medical School at Houston, Houston, Texas 77030, United States
| | - Venkata K P S Mallampalli
- Department of Biochemistry and Molecular Biology and Center for Membrane Biology, University of Texas McGovern Medical School at Houston, Houston, Texas 77030, United States
| | - Stavros Azinas
- Department of Biochemistry and Molecular Biology and Center for Membrane Biology, University of Texas McGovern Medical School at Houston, Houston, Texas 77030, United States
| | - William Dowhan
- Department of Biochemistry and Molecular Biology and Center for Membrane Biology, University of Texas McGovern Medical School at Houston, Houston, Texas 77030, United States
| |
Collapse
|
26
|
Abstract
Due to the heterogenous lipid environment in which integral membrane proteins are embedded, they should follow a set of assembly rules, which govern transmembrane protein folding and topogenesis accordingly to a given lipid profile. Recombinant strains of bacteria have been engineered to have different membrane phospholipid compositions by molecular genetic manipulation of endogenous and foreign genes encoding lipid biosynthetic enzymes. Such strains provide a means to investigate the in vivo role of lipids in many different aspects of membrane function, folding and biogenesis. In vitro and in vivo studies established a function of lipids as molecular chaperones and topological determinants specifically assisting folding and topogenesis of membrane proteins. These results led to the extension of the Positive Inside Rule to Charge Balance Rule, which incorporates a role for lipid-protein interactions in determining membrane protein topological organization at the time of initial membrane insertion and dynamically after initial assembly. Membrane protein topogenesis appears to be a thermodynamically driven process in which lipid-protein interactions affect the potency of charged amino acid residues as topological signals. Dual topology for a membrane protein can be established during initial assembly where folding intermediates in multiple topological conformations are in rapid equilibrium (thus separated by a low activation energy), which is determined by the lipid environment. Post-assembly changes in lipid composition or post-translational modifications can trigger a reorganization of protein topology by inducing destabilization and refolding of a membrane protein. The lipid-dependent dynamic nature of membrane protein organization provides a novel means of regulating protein function.
Collapse
|
27
|
Rimon A, Mondal R, Friedler A, Padan E. Cardiolipin is an Optimal Phospholipid for the Assembly, Stability, and Proper Functionality of the Dimeric Form of NhaA Na +/H + Antiporter. Sci Rep 2019; 9:17662. [PMID: 31776461 PMCID: PMC6881326 DOI: 10.1038/s41598-019-54198-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 11/04/2019] [Indexed: 11/13/2022] Open
Abstract
Cardiolipin (CL) was shown to bound to the dimer interface of NhaA Na+/H+ antiporter. Here, we explore the cardiolipin-NhaA interaction both in vitro and in vivo. Using a novel and straightforward in-vitro assay in which n-dodecyl β-D maltoside (DDM) detergent is used to delipidate the dimer interface and to split the dimers into monomers; the monomers are subsequently exposed to cardiolipin or the other E. coli phospholipids. Most efficient reconstitution of dimers is observed by cardiolipin. This assay is likely to be applicable to future studies of protein–lipid interactions. In-vivo experiments further reveal that cardiolipin is necessary for NhaA survival. Although less efficient phosphatidyl-glycerol (PG) can also reconstitute NhaA monomers to dimers. We also identify a putative cardiolipin binding site. Our observations may contribute to drug design, as human NhaA homologues, which are involved in severe pathologies, might also require specific phospholipids.
Collapse
Affiliation(s)
- Abraham Rimon
- Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, the Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - Ramakanta Mondal
- Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, the Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - Assaf Friedler
- Institute of Chemistry, the Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - Etana Padan
- Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, the Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 91904, Israel.
| |
Collapse
|
28
|
Ehsan M, Kumar A, Mortensen JS, Du Y, Hariharan P, Kumar KK, Ha B, Byrne B, Guan L, Kobilka BK, Loland CJ, Chae PS. Self-Assembly Behaviors of a Penta-Phenylene Maltoside and Its Application for Membrane Protein Study. Chem Asian J 2019; 14:1926-1931. [PMID: 30969484 PMCID: PMC7239035 DOI: 10.1002/asia.201900224] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 03/22/2019] [Indexed: 01/07/2023]
Abstract
We prepared an amphiphile with a penta-phenylene lipophilic group and a branched trimaltoside head group. This new agent, designated penta-phenylene maltoside (PPM), showed a marked tendency to self-assembly into micelles via strong aromatic-aromatic interactions in aqueous media, as evidenced by 1 H NMR spectroscopy and fluorescence studies. When utilized for membrane protein studies, this new agent was superior to DDM, a gold standard conventional detergent, in stabilizing multiple proteins long term. The ability of this agent to form aromatic-aromatic interactions is likely responsible for enhanced protein stabilization when associated with a target membrane protein.
Collapse
Affiliation(s)
- Muhammad Ehsan
- Department of Bionanotechnology, Hanyang University, Ansan, 15588, Korea
- Current address: Department of Chemistry, Mirpur University of Science&Technology (MUST), Mirpur-, 10250 (AJK), Pakistan
| | - Ashwani Kumar
- Department of Bionanotechnology, Hanyang University, Ansan, 15588, Korea
| | - Jonas S Mortensen
- Department of Neuroscience, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Yang Du
- Molecular and Cellular Physiology, Stanford University, Stanford, CA, 94305, USA
| | - Parameswaran Hariharan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center Lubbock, TX, 79430, USA
| | - Kaavya K Kumar
- Molecular and Cellular Physiology, Stanford University, Stanford, CA, 94305, USA
| | - Betty Ha
- Molecular and Cellular Physiology, Stanford University, Stanford, CA, 94305, USA
| | - Bernadette Byrne
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center Lubbock, TX, 79430, USA
| | - Brian K Kobilka
- Molecular and Cellular Physiology, Stanford University, Stanford, CA, 94305, USA
| | - Claus J Loland
- Department of Neuroscience, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Pil Seok Chae
- Department of Bionanotechnology, Hanyang University, Ansan, 15588, Korea
| |
Collapse
|