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Hariharan P, Bakhtiiari A, Liang R, Guan L. Distinct roles of the major binding residues in the cation-binding pocket of the melibiose transporter MelB. J Biol Chem 2024; 300:107427. [PMID: 38823641 PMCID: PMC11259710 DOI: 10.1016/j.jbc.2024.107427] [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: 03/09/2024] [Revised: 05/11/2024] [Accepted: 05/22/2024] [Indexed: 06/03/2024] Open
Abstract
Salmonella enterica serovar Typhimurium melibiose permease (MelBSt) is a prototype of the major facilitator superfamily (MFS) transporters, which play important roles in human health and diseases. MelBSt catalyzed the symport of galactosides with Na+, Li+, or H+ but prefers the coupling with Na+. Previously, we determined the structures of the inward- and outward-facing conformation of MelBSt and the molecular recognition for galactoside and Na+. However, the molecular mechanisms for H+- and Na+-coupled symport remain poorly understood. In this study, we solved two x-ray crystal structures of MelBSt, the cation-binding site mutants D59C at an unliganded apo-state and D55C at a ligand-bound state, and both structures display the outward-facing conformations virtually identical as published. We determined the energetic contributions of three major Na+-binding residues for the selection of Na+ and H+ by free energy simulations. Transport assays showed that the D55C mutant converted MelBSt to a solely H+-coupled symporter, and together with the free-energy perturbation calculation, Asp59 is affirmed to be the sole protonation site of MelBSt. Unexpectedly, the H+-coupled melibiose transport exhibited poor activities at greater bulky ΔpH and better activities at reversal ΔpH, supporting the novel theory of transmembrane-electrostatically localized protons and the associated membrane potential as the primary driving force for the H+-coupled symport mediated by MelBSt. This integrated study of crystal structure, bioenergetics, and free energy simulations, demonstrated the distinct roles of the major binding residues in the cation-binding pocket of MelBSt.
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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, Texas, USA
| | | | - Ruibin Liang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA.
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas, USA.
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2
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Hariharan P, Bakhtiiari A, Liang R, Guan L. Distinct roles of the major binding residues in the cation-binding pocket of MelB. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.27.582382. [PMID: 38464317 PMCID: PMC10925273 DOI: 10.1101/2024.02.27.582382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Salmonella enterica serovar Typhimurium melibiose permease (MelBSt) is a prototype of the major facilitator superfamily (MFS) transporters, which play important roles in human health and diseases. MelBSt catalyzed the symport of galactosides with either H+, Li+, or Na+, but prefers the coupling with Na+. Previously, we determined the structures of the inward- and outward-facing conformation of MelBSt, as well as the molecular recognition for galactoside and Na+. However, the molecular mechanisms for H+- and Na+-coupled symport still remain poorly understood. We have solved two x-ray crystal structures of MelBSt cation-binding site mutants D59C at an unliganded apo-state and D55C at a ligand-bound state, and both structures display the outward-facing conformations virtually identical as published previously. We determined the energetic contributions of three major Na+-binding residues in cation selectivity for Na+ and H+ by the free energy simulations. The D55C mutant converted MelBSt to a solely H+-coupled symporter, and together with the free-energy perturbation calculation, Asp59 is affirmed to be the sole protonation site of MelBSt. Unexpectedly, the H+-coupled melibiose transport with poor activities at higher ΔpH and better activities at reversal ΔpH was observed, supporting that the membrane potential is the primary driving force for the H+-coupled symport mediated by MelBSt. This integrated study of crystal structure, bioenergetics, and free energy simulations, demonstrated the distinct roles of the major binding residues in the cation-binding pocket.
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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
| | | | - Ruibin Liang
- Department of Chemistry and Biochemistry, Texas Tech University, 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
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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.
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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
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Yoon S, Bae HE, Hariharan P, Nygaard A, Lan B, Woubshete M, Sadaf A, Liu X, Loland CJ, Byrne B, Guan L, Chae PS. Rational Approach to Improve Detergent Efficacy for Membrane Protein Stabilization. Bioconjug Chem 2024; 35:223-231. [PMID: 38215010 DOI: 10.1021/acs.bioconjchem.3c00507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2024]
Abstract
Membrane protein structures are essential for the molecular understanding of diverse cellular processes and drug discovery. Detergents are not only widely used to extract membrane proteins from membranes but also utilized to preserve native protein structures in aqueous solution. However, micelles formed by conventional detergents are suboptimal for membrane protein stabilization, necessitating the development of novel amphiphilic molecules with enhanced protein stabilization efficacy. In this study, we prepared two sets of tandem malonate-derived glucoside (TMG) variants, both of which were designed to increase the alkyl chain density in micelle interiors. The alkyl chain density was modulated either by reducing the spacer length (TMG-Ms) or by introducing an additional alkyl chain between the two alkyl chains of the original TMGs (TMG-Ps). When evaluated with a few membrane proteins including a G protein-coupled receptor, TMG-P10,8 was found to be substantially more efficient at extracting membrane proteins and also effective at preserving protein integrity in the long term compared to the previously described TMG-A13. This result reveals that inserting an additional alkyl chain between the two existing alkyl chains is an effective way to optimize detergent properties for membrane protein study. This new biochemical tool and the design principle described have the potential to facilitate membrane protein structure determination.
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Affiliation(s)
- Soyoung Yoon
- Department of Bionano Engineering, Hanyang University ERICA, Ansan 155-88, South Korea
| | - Hyoung Eun Bae
- Department of Bionano Engineering, Hanyang University ERICA, Ansan 155-88, South Korea
| | - 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 79430, United States
| | - Andreas Nygaard
- Department of Neuroscience, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Baoliang Lan
- Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, School of Medicine, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Menebere Woubshete
- Department of Life Sciences, Imperial College London, London SW7 2AZ, U.K
| | - Aiman Sadaf
- Department of Bionano Engineering, Hanyang University ERICA, Ansan 155-88, South Korea
| | - Xiangyu Liu
- Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, School of Medicine, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Claus J Loland
- Department of Neuroscience, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Bernadette Byrne
- Department of Life Sciences, Imperial College London, London SW7 2AZ, U.K
| | - 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 79430, United States
| | - Pil Seok Chae
- Department of Bionano Engineering, Hanyang University ERICA, Ansan 155-88, South Korea
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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.
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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
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Ghani L, Kim S, Ehsan M, Lan B, Poulsen IH, Dev C, Katsube S, Byrne B, Guan L, Loland CJ, Liu X, Im W, Chae PS. Melamine-cored glucosides for membrane protein solubilization and stabilization: importance of water-mediated intermolecular hydrogen bonding in detergent performance. Chem Sci 2023; 14:13014-13024. [PMID: 38023530 PMCID: PMC10664503 DOI: 10.1039/d3sc03543c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 10/22/2023] [Indexed: 12/01/2023] Open
Abstract
Membrane proteins play essential roles in a number of biological processes, and their structures are important in elucidating such processes at the molecular level and also for rational drug design and development. Membrane protein structure determination is notoriously challenging compared to that of soluble proteins, due largely to the inherent instability of their structures in non-lipid environments. Micelles formed by conventional detergents have been widely used for membrane protein manipulation, but they are suboptimal for long-term stability of membrane proteins, making downstream characterization difficult. Hence, there is an unmet need for the development of new amphipathic agents with enhanced efficacy for membrane protein stabilization. In this study, we designed and synthesized a set of glucoside amphiphiles with a melamine core, denoted melamine-cored glucosides (MGs). When evaluated with four membrane proteins (two transporters and two G protein-coupled receptors), MG-C11 conferred notably enhanced stability compared to the commonly used detergents, DDM and LMNG. These promising findings are mainly attributed to a unique feature of the MGs, i.e., the ability to form dynamic water-mediated hydrogen-bond networks between detergent molecules, as supported by molecular dynamics simulations. Thus, MG-C11 is the first example of a non-peptide amphiphile capable of forming intermolecular hydrogen bonds within a protein-detergent complex environment. Detergent micelles formed via a hydrogen-bond network could represent the next generation of highly effective membrane-mimetic systems useful for membrane protein structural studies.
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Affiliation(s)
- Lubna Ghani
- Department of Bionano Engineering, Hanyang University Ansan 155-88 South Korea
| | - Seonghoon Kim
- School of Computational Sciences, Korea Institute for Advanced Study Seoul 024-55 South Korea
| | - Muhammad Ehsan
- Department of Bionano Engineering, Hanyang University Ansan 155-88 South Korea
| | - Baoliang Lan
- Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, School of Medicine, School of Pharmaceutical Sciences, Tsinghua University Beijing 100084 China
| | - Ida H Poulsen
- Department of Neuroscience, University of Copenhagen Copenhagen DK-2200 Denmark
| | - Chandra Dev
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center Lubbock Texas 79430 USA
| | - 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 79430 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 Texas 79430 USA
| | - Claus J Loland
- Department of Neuroscience, University of Copenhagen Copenhagen DK-2200 Denmark
| | - Xiangyu Liu
- Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, School of Medicine, School of Pharmaceutical Sciences, Tsinghua University Beijing 100084 China
| | - Wonpil Im
- Department of Biological Sciences, Chemistry, and Bioengineering Lehigh University Bethlehem PA 18015 USA
| | - Pil Seok Chae
- Department of Bionano Engineering, Hanyang University Ansan 155-88 South Korea
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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: 0] [Impact Index Per Article: 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.
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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.
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Yao J, Wang ZN, Liu H, Jin H, Zhang Y. Survey of Acetylation for Thermoanaerobacter tengcongensis. Appl Biochem Biotechnol 2023; 195:6081-6097. [PMID: 36809429 DOI: 10.1007/s12010-023-04361-9] [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] [Accepted: 01/10/2023] [Indexed: 02/23/2023]
Abstract
Non-histone protein acetylation is involved in key cellular processes both in eukaryotes and prokaryotes. Acetylation in bacteria is used to modify proteins involved in metabolism and allow the bacteria to adapt to their environment. TTE (Thermoanaerobacter tengcongensis) is an anaerobic, thermophilic saccharolytic bacterium that grows at extreme temperature range between 50 and 80 ℃. The annotated TTE proteome contains less than 3000 proteins. We analyzed the proteome and acetylome of TTE using 2DLC-MS/MS (2-dimensional liquid chromatography mass spectrum). We evaluated the ability of mass spectrometry technology to cover a relatively small proteome as much as possible. And we also observed wide spread of acetylation in TTE, which changed under different temperatures. A total of 2082 proteins were identified, which accounts for about 82% of the database. A total of 2050 (~ 98%) proteins were quantified in at least one culture condition and 1818 proteins were quantified in all 4 conditions. The result also consisted 3457 acetylation sites corresponding to 827 distinct proteins, which covered 40% of the proteins identified. Bioinformatics analysis reported that proteins related to replication, recombination, repair, and extracellular structure cell wall biogenesis had more than half members acetylated, while energy production, carbohydrate transport, and metabolism related proteins were least acetylated. Our result suggested that acetylation affects the ATP-related energy metabolism and energy-dependent biosynthesis process. Comparing the enzymes related with lysine acetylation and acetyl-CoA (acetyl-coenzyme A) metabolism, we suggested that the acetylation of TTE took a non-enzymatic mechanism and affected by abundance of acetyl-CoA.
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Affiliation(s)
- Jun Yao
- Department of Chemistry, Shanghai Stomatological Hospital & Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China
| | - Ze-Ning Wang
- Department of Chemistry, Shanghai Stomatological Hospital & Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China
| | - Hang Liu
- Department of Chemistry, Shanghai Stomatological Hospital & Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China
| | - Hong Jin
- Department of Chemistry, Shanghai Stomatological Hospital & Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China.
| | - Yang Zhang
- Department of Chemistry, Shanghai Stomatological Hospital & Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China.
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9
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Katsube S, Willibal K, Vemulapally S, Hariharan P, Tikhonova E, Pardon E, Kaback HR, Steyaert J, Guan L. In vivo and in vitro characterizations of melibiose permease (MelB) conformation-dependent nanobodies reveal sugar-binding mechanisms. J Biol Chem 2023; 299:104967. [PMID: 37380079 PMCID: PMC10374971 DOI: 10.1016/j.jbc.2023.104967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 06/13/2023] [Accepted: 06/19/2023] [Indexed: 06/30/2023] Open
Abstract
Salmonella enterica serovar Typhimurium melibiose permease (MelBSt) is a prototype of the Na+-coupled major facilitator superfamily transporters, which are important for the cellular uptake of molecules including sugars and small drugs. Although the symport mechanisms have been well-studied, mechanisms of substrate binding and translocation remain enigmatic. We have previously determined the sugar-binding site of outward-facing MelBSt by crystallography. To obtain other key kinetic states, here we raised camelid single-domain nanobodies (Nbs) and carried out a screening against the WT MelBSt under 4 ligand conditions. We applied an in vivo cAMP-dependent two-hybrid assay to detect interactions of Nbs with MelBSt and melibiose transport assays to determine the effects on MelBSt functions. We found that all selected Nbs showed partial to complete inhibitions of MelBSt transport activities, confirming their intracellular interactions. A group of Nbs (714, 725, and 733) was purified, and isothermal titration calorimetry measurements showed that their binding affinities were significantly inhibited by the substrate melibiose. When titrating melibiose to the MelBSt/Nb complexes, Nb also inhibited the sugar-binding. However, the Nb733/MelBSt complex retained binding to the coupling cation Na+ and also to the regulatory enzyme EIIAGlc of the glucose-specific phosphoenolpyruvate/sugar phosphotransferase system. Further, EIIAGlc/MelBSt complex also retained binding to Nb733 and formed a stable supercomplex. All data indicated that MelBSt trapped by Nbs retained its physiological functions and the trapped conformation is similar to that bound by the physiological regulator EIIAGlc. Therefore, these conformational Nbs can be useful tools for further structural, functional, and conformational analyses.
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Affiliation(s)
- Satoshi Katsube
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas, USA
| | - Katleen Willibal
- VIB Center for Structural Biology Research, VIB, Brussel, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, Brussel, Belgium
| | - Sangama Vemulapally
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas, USA
| | - Parameswaran Hariharan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas, USA
| | - Elena Tikhonova
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas, USA
| | - Els Pardon
- VIB Center for Structural Biology Research, VIB, Brussel, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, Brussel, Belgium
| | - H Ronald Kaback
- Department of Physiology and Department of Microbiology, Immunology, and Molecular Genetics, Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California, USA
| | - Jan Steyaert
- VIB Center for Structural Biology Research, VIB, Brussel, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, Brussel, Belgium
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas, USA.
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10
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Katsube S, Sakai K, Ando T, Tobe R, Yoneyama H. l-Alanine Exporter AlaE Functions as One of the d-Alanine Exporters in Escherichia coli. Int J Mol Sci 2023; 24:10242. [PMID: 37373388 DOI: 10.3390/ijms241210242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
d-amino acids have recently been found to be present in the extracellular milieu at millimolar levels and are therefore assumed to play a physiological function. However, the pathway (or potential pathways) by which these d-amino acids are secreted remains unknown. Recently, Escherichia coli has been found to possess one or more energy-dependent d-alanine export systems. To gain insight into these systems, we developed a novel screening system in which cells expressing a putative d-alanine exporter could support the growth of d-alanine auxotrophs in the presence of l-alanyl-l-alanine. In the initial screening, five d-alanine exporter candidates, AlaE, YmcD, YciC, YraM, and YidH, were identified. Transport assays of radiolabeled d-alanine in cells expressing these candidates indicated that YciC and AlaE resulted in lower intracellular levels of d-alanine. Further detailed transport assays of AlaE in intact cells showed that it exports d-alanine in an expression-dependent manner. In addition, the growth constraints on cells in the presence of 90 mM d-alanine were mitigated by the overexpression of AlaE, implying that AlaE could export free d-alanine in addition to l-alanine under conditions in which intracellular d/l-alanine levels are raised. This study also shows, for the first time, that YciC could function as a d-alanine exporter in intact cells.
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Affiliation(s)
- Satoshi Katsube
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Keiichiro Sakai
- Laboratory of Animal Microbiology, Department of Animal Science, Graduate School of Agricultural Science, Tohoku University, 468-1, Aramaki Aza Aoba, Aoba-ku, Sendai 980-0845, Japan
| | - Tasuke Ando
- Laboratory of Animal Microbiology, Department of Animal Science, Graduate School of Agricultural Science, Tohoku University, 468-1, Aramaki Aza Aoba, Aoba-ku, Sendai 980-0845, Japan
| | - Ryuta Tobe
- Laboratory of Animal Microbiology, Department of Animal Science, Graduate School of Agricultural Science, Tohoku University, 468-1, Aramaki Aza Aoba, Aoba-ku, Sendai 980-0845, Japan
| | - Hiroshi Yoneyama
- Laboratory of Animal Microbiology, Department of Animal Science, Graduate School of Agricultural Science, Tohoku University, 468-1, Aramaki Aza Aoba, Aoba-ku, Sendai 980-0845, Japan
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11
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Ghani L, Zhang X, Munk CF, Hariharan P, Lan B, Yun HS, Byrne B, Guan L, Loland CJ, Liu X, Chae PS. Tris(hydroxymethyl)aminomethane Linker-Bearing Triazine-Based Triglucosides for Solubilization and Stabilization of Membrane Proteins. Bioconjug Chem 2023; 34:739-747. [PMID: 36919927 PMCID: PMC10145683 DOI: 10.1021/acs.bioconjchem.3c00042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/21/2023] [Indexed: 03/16/2023]
Abstract
High-resolution membrane protein structures are essential for a fundamental understanding of the molecular basis of diverse cellular processes and for drug discovery. Detergents are widely used to extract membrane-spanning proteins from membranes and maintain them in a functional state for downstream characterization. Due to limited long-term stability of membrane proteins encapsulated in conventional detergents, development of novel agents is required to facilitate membrane protein structural study. In the current study, we designed and synthesized tris(hydroxymethyl)aminomethane linker-bearing triazine-based triglucosides (TTGs) for solubilization and stabilization of membrane proteins. When these glucoside detergents were evaluated for four membrane proteins including two G protein-coupled receptors, a few TTGs including TTG-C10 and TTG-C11 displayed markedly enhanced behaviors toward membrane protein stability relative to two maltoside detergents [DDM (n-dodecyl-β-d-maltoside) and LMNG (lauryl maltose neopentyl glycol)]. This is a notable feature of the TTGs as glucoside detergents tend to be inferior to maltoside detergents at stabilizing membrane proteins. The favorable behavior of the TTGs for membrane protein stability is likely due to the high hydrophobicity of the lipophilic groups, an optimal range of hydrophilic-lipophilic balance, and the absence of cis-trans isomerism.
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Affiliation(s)
- Lubna Ghani
- Department
of Bionano Engineering, Hanyang University, Ansan 155-88, South Korea
| | - Xiang Zhang
- Tsinghua-Peking
Center for Life Sciences, Beijing Frontier Research Center for Biological
Structure, Beijing Advanced Innovation Center for Structural Biology,
School of Medicine, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Chastine F. Munk
- Department
of Neuroscience, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - 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 79430, United States
| | - Baoliang Lan
- Tsinghua-Peking
Center for Life Sciences, Beijing Frontier Research Center for Biological
Structure, Beijing Advanced Innovation Center for Structural Biology,
School of Medicine, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Hong Sik Yun
- Department
of Bionano Engineering, Hanyang University, Ansan 155-88, South Korea
| | - Bernadette Byrne
- Department
of Life Sciences, Imperial College London, London SW7 2AZ, U.K.
| | - 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 79430, United States
| | - Claus J. Loland
- Department
of Neuroscience, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Xiangyu Liu
- Tsinghua-Peking
Center for Life Sciences, Beijing Frontier Research Center for Biological
Structure, Beijing Advanced Innovation Center for Structural Biology,
School of Medicine, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Pil Seok Chae
- Department
of Bionano Engineering, Hanyang University, Ansan 155-88, South Korea
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12
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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: 0] [Impact Index Per Article: 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.
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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.
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13
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Lee HJ, Ehsan M, Zhang X, Katsube S, Munk CF, Wang H, Ahmed W, Kumar A, Byrne B, Loland CJ, Guan L, Liu X, Chae PS. Development of 1,3-acetonedicarboxylate-derived glucoside amphiphiles (ACAs) for membrane protein study. Chem Sci 2022; 13:5750-5759. [PMID: 35694361 PMCID: PMC9116450 DOI: 10.1039/d2sc00539e] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 04/02/2022] [Indexed: 12/31/2022] Open
Abstract
Detergents are extensively used for membrane protein manipulation. Membrane proteins solubilized in conventional detergents are prone to denaturation and aggregation, rendering downstream characterization of these bio-macromolecules difficult. Although many amphiphiles have been developed to overcome the limited efficacy of conventional detergents for protein stabilization, only a handful of novel detergents have so far proved useful for membrane protein structural studies. Here, we introduce 1,3-acetonedicarboxylate-derived amphiphiles (ACAs) containing three glucose units and two alkyl chains as head and tail groups, respectively. The ACAs incorporate two different patterns of alkyl chain attachment to the core detergent unit, generating two sets of amphiphiles: ACA-As (asymmetrically alkylated) and ACA-Ss (symmetrically alkylated). The difference in the attachment pattern of the detergent alkyl chains resulted in minor variation in detergent properties such as micelle size, critical micelle concentration, and detergent behaviors toward membrane protein extraction and stabilization. In contrast, the impact of the detergent alkyl chain length on protein stability was marked. The two C11 variants (ACA-AC11 and ACA-SC11) were most effective at stabilizing the tested membrane proteins. The current study not only introduces new glucosides as tools for membrane protein study, but also provides detergent structure–property relationships important for future design of novel amphiphiles. Newly developed amphiphiles, designated ACAs, are not only efficient at extracting G protein-coupled receptors from the membranes, but also conferred enhanced stability to the receptors compared to the gold standards (DDM and LMNG).![]()
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Affiliation(s)
- Ho Jin Lee
- Department of Bionano Engineering, Hanyang University Ansan 155-88 Korea
| | - Muhammad Ehsan
- Department of Bionano Engineering, Hanyang University Ansan 155-88 Korea
| | - Xiang Zhang
- Beijing Advanced Innovation Center for Structural Biology, School of Medicine, School of Pharmaceutical Sciences, Tsinghua University 100084 Beijing China
| | - Satoshi Katsube
- 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
| | - Chastine F Munk
- Department of Neuroscience, University of Copenhagen Copenhagen DK-2200 Denmark
| | - Haoqing Wang
- Department of Molecular and Cellular Physiology, Stanford University California 94305 USA
| | - Waqar Ahmed
- Department of Bionano Engineering, Hanyang University Ansan 155-88 Korea
| | - Ashwani Kumar
- Department of Bionano Engineering, Hanyang University Ansan 155-88 Korea
| | - Bernadette Byrne
- Department of Life Sciences, Imperial College London London SW7 2AZ UK
| | - Claus J Loland
- Department of Neuroscience, University of Copenhagen Copenhagen DK-2200 Denmark
| | - 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
| | - Xiangyu Liu
- Beijing Advanced Innovation Center for Structural Biology, School of Medicine, School of Pharmaceutical Sciences, Tsinghua University 100084 Beijing China
| | - Pil Seok Chae
- Department of Bionano Engineering, Hanyang University Ansan 155-88 Korea
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14
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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]
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15
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Ehsan M, Wang H, Katsube S, Munk CF, Du Y, Youn T, Yoon S, Byrne B, Loland CJ, Guan L, Kobilka BK, Chae PS. Glyco-steroidal amphiphiles (GSAs) for membrane protein structural study. Chembiochem 2022; 23:e202200027. [PMID: 35129249 PMCID: PMC8986615 DOI: 10.1002/cbic.202200027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/05/2022] [Indexed: 11/08/2022]
Abstract
Integral membrane proteins pose considerable challenges to high resolution structural analysis. Maintaining membrane proteins in their native state during protein isolation is essential for structural study of these bio-macromolecules. Detergents are the most commonly used amphiphilic compounds for stabilizing membrane proteins in solution outside a lipid bilayer. We previously introduced a glyco-diosgenin (GDN) detergent that was shown to be highly effective at stabilizing a wide range of membrane proteins. This steroidal detergent has additionally gained attention due to its compatibility with membrane protein structure study via cryo-EM. However, synthetic inconvenience limits widespread use of GDN in membrane protein study. To improve its synthetic accessibility and to further enhance detergent efficacy for protein stabilization, we designed a new class of glyco-steroid-based detergents using three steroid units: cholestanol, cholesterol and diosgenin. These new detergents were efficiently prepared and showed marked efficacy for protein stabilization in evaluation with a few model membrane proteins including two G protein-coupled receptors. Some new agents were not only superior to a gold standard detergent, DDM, but were also more effective than the original GDN at preserving protein integrity long term. These agents represent valuable alternatives to GDN, and are likely to facilitate structural determination of challenging membrane proteins.
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Affiliation(s)
- Muhammad Ehsan
- Hanyang University, Department of Bionano Engineering, KOREA, REPUBLIC OF
| | - Haoqing Wang
- Stanford University, Department of Molecular and Cellular Physiology, UNITED STATES
| | - Satoshi Katsube
- Texas Tech University, Department of Cell Physiology and Molecular Biophysics, UNITED STATES
| | - Chastine F Munk
- University of Copenhagen: Kobenhavns Universitet, Department of Neuroscience, DENMARK
| | - Yang Du
- Stanford University, Department of Molecular and Cellular Physiology, UNITED STATES
| | - Taeyeol Youn
- Hanyang University, Department of Bionano Engineering, KOREA, REPUBLIC OF
| | - Soyoung Yoon
- Hanyang University, Department of Bionano Engineering, KOREA, REPUBLIC OF
| | - Bernadette Byrne
- Imperial College London, Department of Life Sciences, UNITED KINGDOM
| | - Claus J Loland
- University of Copenhagen: Kobenhavns Universitet, Department of Neurosciences, DENMARK
| | - Lan Guan
- Texas Tech University, Department of Cell Physiology and Molecular Biophysics, UNITED STATES
| | - Brian K Kobilka
- Stanford University, Department of Molecular and Cellular Physiology, UNITED STATES
| | - Pil Seok Chae
- Hanyang University, Department of Bionano Engineering, 55 Hanyangdaehak-ro, 426-791, Ansan, KOREA, REPUBLIC OF
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16
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Neves AT, Stenner R, Race PR, Curnow P. Expression, purification and preliminary characterisation of the choline transporter LicB from opportunistic bacterial pathogens. Protein Expr Purif 2021; 190:106011. [PMID: 34737041 DOI: 10.1016/j.pep.2021.106011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/19/2021] [Accepted: 10/31/2021] [Indexed: 11/28/2022]
Abstract
Many opportunistic bacteria that infect the upper respiratory tract decorate their cell surface with phosphorylcholine to support colonisation and outgrowth. These surface modifications require the active import of choline from the host environment, a process thought to be mediated by a family of dedicated integral membrane proteins that act as choline permeases. Here, we present the expression and purification of the archetype of these choline transporters, LicB from Haemophilus influenzae. We show that LicB can be recombinantly produced in Escherichia coli and purified to homogeneity in a stable, folded state using the detergent n-dodecyl-β-d-maltopyranoside. Equilibrium binding studies with the fluorescent ligand dansylcholine suggest that LicB is selective towards choline, with reduced affinity for acetylcholine and no apparent activity towards other small molecules including glycine, carnitine and betaine. We also identify a conserved sequence motif within the LicB family and show that mutations within this motif compromise protein structure and function. Our results are consistent with previous observations that LicB is a specific high-affinity choline transporter, and provide an experimental platform for further studies of this permease family.
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Affiliation(s)
| | | | - Paul R Race
- School of Biochemistry, University of Bristol, UK
| | - Paul Curnow
- School of Biochemistry, University of Bristol, UK.
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17
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Ehsan M, Wang H, Cecchetti C, Mortensen JS, Du Y, Hariharan P, Nygaard A, Lee HJ, Ghani L, Guan L, Loland CJ, Byrne B, Kobilka BK, Chae PS. Maltose-bis(hydroxymethyl)phenol (MBPs) and Maltose-tris(hydroxymethyl)phenol (MTPs) Amphiphiles for Membrane Protein Stability. ACS Chem Biol 2021; 16:1779-1790. [PMID: 34445864 DOI: 10.1021/acschembio.1c00578] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Membrane protein structures provide a fundamental understanding of their molecular actions and are of importance for drug development. Detergents are widely used to solubilize, stabilize, and crystallize membrane proteins, but membrane proteins solubilized in conventional detergents are prone to denaturation and aggregation. Thus, developing novel detergents with enhanced efficacy for protein stabilization remains important. We report herein the design and synthesis of a class of phenol-derived maltoside detergents. Using two different linkers, we prepared two sets of new detergents, designated maltose-bis(hydroxymethyl)phenol (MBPs) and maltose-tris(hydroxymethyl)phenol (MTPs). The evaluation of these detergents with three transporters and two G-protein coupled receptors allowed us to identify a couple of new detergents (MBP-C9 and MTP-C12) that consistently conferred enhanced stability to all tested proteins compared to a gold standard detergent (DDM). Furthermore, the data analysis based on the detergent structures provides key detergent features responsible for membrane protein stabilization that together will facilitate the future design of novel detergents.
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Affiliation(s)
- Muhammad Ehsan
- Department of Bionano Engineering, Center for Bionano Intelligence Education and Research, Hanyang University, Ansan 155-88, South Korea
| | - Haoqing Wang
- Department of Molecular and Cellular Physiology, Stanford University, California 94305, United States
| | - Cristina Cecchetti
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Jonas S. Mortensen
- Department of Neuroscience, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Yang Du
- Department of Molecular and Cellular Physiology, Stanford University, California 94305, United States
| | - 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 79430, United States
| | - Andreas Nygaard
- Department of Neuroscience, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Ho Jin Lee
- Department of Bionano Engineering, Center for Bionano Intelligence Education and Research, Hanyang University, Ansan 155-88, South Korea
| | - Lubna Ghani
- Department of Bionano Engineering, Center for Bionano Intelligence Education and Research, Hanyang University, Ansan 155-88, South Korea
| | - 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 79430, United States
| | - Claus J. Loland
- Department of Neuroscience, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Bernadette Byrne
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Brian K. Kobilka
- Department of Molecular and Cellular Physiology, Stanford University, California 94305, United States
| | - Pil Seok Chae
- Department of Bionano Engineering, Center for Bionano Intelligence Education and Research, Hanyang University, Ansan 155-88, South Korea
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18
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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: 1] [Impact Index Per Article: 0.3] [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.
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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.
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19
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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: 18] [Impact Index Per Article: 6.0] [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.
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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
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20
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Conformationally flexible core-bearing detergents with a hydrophobic or hydrophilic pendant: Effect of pendant polarity on detergent conformation and membrane protein stability. Acta Biomater 2021; 128:393-407. [PMID: 33933694 DOI: 10.1016/j.actbio.2021.04.043] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/31/2021] [Accepted: 04/21/2021] [Indexed: 02/06/2023]
Abstract
Membrane protein structures provide atomic level insight into essential biochemical processes and facilitate protein structure-based drug design. However, the inherent instability of these bio-macromolecules outside lipid bilayers hampers their structural and functional study. Detergent micelles can be used to solubilize and stabilize these membrane-inserted proteins in aqueous solution, thereby enabling their downstream characterizations. Membrane proteins encapsulated in detergent micelles tend to denature and aggregate over time, highlighting the need for development of new amphiphiles effective for protein solubility and stability. In this work, we present newly-designed maltoside detergents containing a pendant chain attached to a glycerol-decorated tris(hydroxymethyl)methane (THM) core, designated GTMs. One set of the GTMs has a hydrophobic pendant (ethyl chain; E-GTMs), and the other set has a hydrophilic pendant (methoxyethoxylmethyl chain; M-GTMs) placed in the hydrophobic-hydrophilic interfaces. The two sets of GTMs displayed profoundly different behaviors in terms of detergent self-assembly and protein stabilization efficacy. These behaviors mainly arise from the polarity difference between two pendants (ethyl and methoxyethoxylmethyl chains) that results in a large variation in detergent conformation between these sets of GTMs in aqueous media. The resulting high hydrophobic density in the detergent micelle interior is likely responsible for enhanced efficacy of the M-GTMs for protein stabilization compared to the E-GTMs and a gold standard detergent DDM. A representative GTM, M-GTM-O12, was more effective for protein stability than some recently developed detergents including LMNG. This is the first case study investigating the effect of pendant polarity on detergent geometry correlated with detergent efficacy for protein stabilization. STATEMENT OF SIGNIFICANCE: This study introduces new amphiphiles for use as biochemical tools in membrane protein studies. We identified a few hydrophilic pendant-bearing amphiphiles such as M-GTM-O11 and M-GTM-O12 that show remarkable efficacy for membrane protein solubilization and stabilization compared to a gold standard DDM, the hydrophobic counterparts (E-GTMs) and a significantly optimized detergent LMNG. In addition, detergent results obtained in the current study reveals the effect of detergent pendant polarity on protein solubility and stability. Thus, the current study represents both significant chemical and conceptual advance. The detergent tools and design principle introduced here advance protein science and facilitate structure-based drug design and development.
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21
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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: 3] [Impact Index Per Article: 1.0] [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.
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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
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22
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Rybenkov VV, Zgurskaya HI, Ganguly C, Leus IV, Zhang Z, Moniruzzaman M. The Whole Is Bigger than the Sum of Its Parts: Drug Transport in the Context of Two Membranes with Active Efflux. Chem Rev 2021; 121:5597-5631. [PMID: 33596653 DOI: 10.1021/acs.chemrev.0c01137] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cell envelope plays a dual role in the life of bacteria by simultaneously protecting it from a hostile environment and facilitating access to beneficial molecules. At the heart of this ability lie the restrictive properties of the cellular membrane augmented by efflux transporters, which preclude intracellular penetration of most molecules except with the help of specialized uptake mediators. Recently, kinetic properties of the cell envelope came into focus driven on one hand by the urgent need in new antibiotics and, on the other hand, by experimental and theoretical advances in studies of transmembrane transport. A notable result from these studies is the development of a kinetic formalism that integrates the Michaelis-Menten behavior of individual transporters with transmembrane diffusion and offers a quantitative basis for the analysis of intracellular penetration of bioactive compounds. This review surveys key experimental and computational approaches to the investigation of transport by individual translocators and in whole cells, summarizes key findings from these studies and outlines implications for antibiotic discovery. Special emphasis is placed on Gram-negative bacteria, whose envelope contains two separate membranes. This feature sets these organisms apart from Gram-positive bacteria and eukaryotic cells by providing them with full benefits of the synergy between slow transmembrane diffusion and active efflux.
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Affiliation(s)
- Valentin V Rybenkov
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Chhandosee Ganguly
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Inga V Leus
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Zhen Zhang
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Mohammad Moniruzzaman
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
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23
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Das M, Mahler F, Hariharan P, Wang H, Du Y, Mortensen JS, Patallo EP, Ghani L, Glück D, Lee HJ, Byrne B, Loland CJ, Guan L, Kobilka BK, Keller S, Chae PS. Diastereomeric Cyclopentane-Based Maltosides (CPMs) as Tools for Membrane Protein Study. J Am Chem Soc 2020; 142:21382-21392. [PMID: 33315387 DOI: 10.1021/jacs.0c09629] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Amphiphilic agents, called detergents, are invaluable tools for studying membrane proteins. However, membrane proteins encapsulated by conventional head-to-tail detergents tend to denature or aggregate, necessitating the development of structurally distinct molecules with improved efficacy. Here, a novel class of diastereomeric detergents with a cyclopentane core unit, designated cyclopentane-based maltosides (CPMs), were prepared and evaluated for their ability to solubilize and stabilize several model membrane proteins. A couple of CPMs displayed enhanced behavior compared with the benchmark conventional detergent, n-dodecyl-β-d-maltoside (DDM), for all the tested membrane proteins including two G-protein-coupled receptors (GPCRs). Furthermore, CPM-C12 was notable for its ability to confer enhanced membrane protein stability compared with the previously developed conformationally rigid NBMs [J. Am. Chem. Soc. 2017, 139, 3072] and LMNG. The effect of the individual CPMs on protein stability varied depending on both the detergent configuration (cis/trans) and alkyl chain length, allowing us draw conclusions on the detergent structure-property-efficacy relationship. Thus, this study not only provides novel detergent tools useful for membrane protein research but also reports on structural features of the detergents critical for detergent efficacy in stabilizing membrane proteins.
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Affiliation(s)
- Manabendra Das
- Department of Bionanotechnology, Center for Bionano Intelligence Education and Research, Hanyang University, Ansan 155-88, Korea.,Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany
| | - Florian Mahler
- Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany
| | - 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 79430, United States
| | - Haoqing Wang
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, California 94305, United States
| | - Yang Du
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, California 94305, United States
| | - Jonas S Mortensen
- Department of Neuroscience, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Eugenio Pérez Patallo
- Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany
| | - Lubna Ghani
- Department of Bionanotechnology, Center for Bionano Intelligence Education and Research, Hanyang University, Ansan 155-88, Korea
| | - David Glück
- Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany
| | - Ho Jin Lee
- Department of Bionanotechnology, Center for Bionano Intelligence Education and Research, Hanyang University, Ansan 155-88, Korea
| | - Bernadette Byrne
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Claus J Loland
- Department of Neuroscience, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - 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 79430, United States
| | - Brian K Kobilka
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, California 94305, United States
| | - Sandro Keller
- Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany.,Institute of Molecular Biosciences (IMB), NAWI Graz, University of Graz, Humboldtstr. 50/III, 8010 Graz, Austria.,Field of Excellence BioHealth, University of Graz, 8010 Graz, Austria.,BioTechMed-Graz, Graz, Austria
| | - Pil Seok Chae
- Department of Bionanotechnology, Center for Bionano Intelligence Education and Research, Hanyang University, Ansan 155-88, Korea
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24
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Bae HE, Cecchetti C, Du Y, Katsube S, Mortensen JS, Huang W, Rehan S, Lee HJ, Loland CJ, Guan L, Kobilka BK, Byrne B, Chae PS. Pendant-bearing glucose-neopentyl glycol (P-GNG) amphiphiles for membrane protein manipulation: Importance of detergent pendant chain for protein stabilization. Acta Biomater 2020; 112:250-261. [PMID: 32522715 PMCID: PMC7366829 DOI: 10.1016/j.actbio.2020.06.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 05/31/2020] [Accepted: 06/02/2020] [Indexed: 12/15/2022]
Abstract
Glucoside detergents are successfully used for membrane protein crystallization mainly because of their ability to form small protein-detergent complexes. In a previous study, we introduced glucose neopentyl glycol (GNG) amphiphiles with a branched diglucoside structure that has facilitated high resolution crystallographic structure determination of several membrane proteins. Like other glucoside detergents, however, these GNGs were less successful than DDM in stabilizing membrane proteins, limiting their wide use in protein structural study. As a strategy to improve GNG efficacy for protein stabilization, we introduced two different alkyl chains (i.e., main and pendant chains) into the GNG scaffold while maintaining the branched diglucoside head group. Of these pendant-bearing GNGs (P-GNGs), three detergents (GNG-2,14, GNG-3,13 and GNG-3,14) were not only notably better than both DDM (a gold standard detergent) and the previously described GNGs at stabilizing all six membrane proteins tested here, but were also as efficient as DDM at membrane protein extraction. The results suggest that the C14 main chain of the P-GNGs is highly compatible with the hydrophobic widths of membrane proteins, while the C2/C3 pendant chain is effective at strengthening detergent hydrophobic interactions. Based on the marked effect on protein stability and solubility, these glucoside detergents hold significant potential for membrane protein structural study. Furthermore, the independent roles of the detergent two alkyl chains first introduced in this study have shed light on new amphiphile design for membrane protein study. STATEMENT OF SIGNIFICANCE: Detergent efficacy for protein stabilization tends to be protein-specific, thus it is challenging to find a detergent that is effective at stabilizing multiple membrane proteins. By incorporating a pendant chain into our previous GNG scaffold, we prepared pendant chain-bearing GNGs (P-GNGs) and identified three P-GNGs that were highly effective at stabilizing all membrane proteins tested here including two GPCRs. In addition, the new detergents were as efficient as DDM at extracting membrane proteins, enabling use of these detergents over the multiple steps of protein isolation. The key difference between the P-GNGs and other glucoside detergents, the presence of a pendant chain, is likely to be responsible for their markedly enhanced protein stabilization behavior.
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Affiliation(s)
- Hyoung Eun Bae
- Department of Bionanotechnology, Hanyang University, Ansan, 15588 (Korea)
| | - Cristina Cecchetti
- Department of Life Sciences, Imperial College London, London, SW7 2AZ (UK)
| | - Yang Du
- Department of Molecular and Cellular Physiology, Stanford University, CA 94305 (USA)
| | - Satoshi Katsube
- 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)
| | - Jonas S Mortensen
- Department of Neuroscience, University of Copenhagen, Copenhagen, DK-2200 (Denmark)
| | - Weijiao Huang
- Department of Molecular and Cellular Physiology, Stanford University, CA 94305 (USA)
| | - Shahid Rehan
- Institute of Biotechnology, University of Helsinki, Helsinki (Finland); HiLIFE, University of Helsinki, Helsinki (Finland)
| | - Ho Jin Lee
- Department of Bionanotechnology, Hanyang University, Ansan, 15588 (Korea)
| | - Claus J Loland
- Department of Neuroscience, University of Copenhagen, Copenhagen, DK-2200 (Denmark)
| | - 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
- Department of Molecular and Cellular Physiology, Stanford University, CA 94305 (USA)
| | - Bernadette Byrne
- Department of Life Sciences, Imperial College London, London, SW7 2AZ (UK)
| | - Pil Seok Chae
- Department of Bionanotechnology, Hanyang University, Ansan, 15588 (Korea).
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25
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Ehsan M, Katsube S, Cecchetti C, Du Y, Mortensen JS, Wang H, Nygaard A, Ghani L, Loland CJ, Kobilka BK, Byrne B, Guan L, Chae PS. New Malonate-Derived Tetraglucoside Detergents for Membrane Protein Stability. ACS Chem Biol 2020; 15:1697-1707. [PMID: 32501004 DOI: 10.1021/acschembio.0c00316] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Membrane proteins are widely studied in detergent micelles, a membrane-mimetic system formed by amphiphilic compounds. However, classical detergents have serious limitations in their utility, particularly for unstable proteins such as eukaryotic membrane proteins and membrane protein complexes, and thus, there is an unmet need for novel amphiphiles with enhanced ability to stabilize membrane proteins. Here, we developed a new class of malonate-derived detergents with four glucosides, designated malonate-derived tetra-glucosides (MTGs), and compared these new detergents with previously reported octyl glucose neopentyl glycol (OGNG) and n-dodecyl-β-d-maltoside (DDM). When tested with two G-protein coupled receptors (GPCRs) and three transporters, a couple of MTGs consistently conferred enhanced stability to all tested proteins compared to DDM and OGNG. As a result of favorable behaviors for a range of membrane proteins, these MTGs have substantial potential for membrane protein research. This study additionally provides a new detergent design principle based on the effect of a polar functional group (i.e., ether) on protein stability depending on its position in the detergent scaffold.
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Affiliation(s)
- Muhammad Ehsan
- Department of Bionanotechnology, Hanyang University, Ansan, 15588, Korea
| | - 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 79430, United States
| | - Cristina Cecchetti
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Yang Du
- School of Life and Health Sciences, Kobilka Institute of Innovative Drug Discovery, Chinese University of Hong Kong, 2001 Longxiang Avenue, Shenzhen, Guangdong 518172, China
| | - Jonas S. Mortensen
- Department of Neuroscience, University of Copenhagen, Copenhagen, DK-2200, Denmark
| | - Haoqing Wang
- Molecular and Cellular Physiology, Stanford University, Stanford, California 94305, United States
| | - Andreas Nygaard
- Department of Neuroscience, University of Copenhagen, Copenhagen, DK-2200, Denmark
| | - Lubna Ghani
- Department of Bionanotechnology, Hanyang University, Ansan, 15588, Korea
| | - Claus J. Loland
- Department of Neuroscience, University of Copenhagen, Copenhagen, DK-2200, Denmark
| | - Brian K. Kobilka
- Molecular and Cellular Physiology, Stanford University, Stanford, California 94305, United States
| | - Bernadette Byrne
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, United Kingdom
| | - 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 79430, United States
| | - Pil Seok Chae
- Department of Bionanotechnology, Hanyang University, Ansan, 15588, Korea
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26
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Ghani L, Munk CF, Zhang X, Katsube S, Du Y, Cecchetti C, Huang W, Bae HE, Saouros S, Ehsan M, Guan L, Liu X, Loland CJ, Kobilka BK, Byrne B, Chae PS. 1,3,5-Triazine-Cored Maltoside Amphiphiles for Membrane Protein Extraction and Stabilization. J Am Chem Soc 2019; 141:19677-19687. [PMID: 31809039 DOI: 10.1021/jacs.9b07883] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Despite their major biological and pharmacological significance, the structural and functional study of membrane proteins remains a significant challenge. A main issue is the isolation of these proteins in a stable and functional state from native lipid membranes. Detergents are amphiphilic compounds widely used to extract membrane proteins from the native membranes and maintain them in a stable form during downstream analysis. However, due to limitations of conventional detergents, it is essential to develop novel amphiphiles with optimal properties for protein stability in order to advance membrane protein research. Here we designed and synthesized 1,3,5-triazine-cored dimaltoside amphiphiles derived from cyanuric chloride. By introducing variations in the alkyl chain linkage (ether/thioether) and an amine-functionalized diol linker (serinol/diethanolamine), we prepared two sets of 1,3,5-triazine-based detergents. When tested with several model membrane proteins, these agents showed remarkable efficacy in stabilizing three transporters and two G protein-coupled receptors. Detergent behavior substantially varied depending on the detergent structural variation, allowing us to explore detergent structure-property-efficacy relationships. The 1,3,5-triazine-based detergents introduced here have significant potential for membrane protein study as a consequence of their structural diversity and universal stabilization efficacy for several membrane proteins.
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Affiliation(s)
- Lubna Ghani
- Department of Bionanotechnology , Hanyang University , Ansan 155-88 , Korea
| | - Chastine F Munk
- Department of Neuroscience , University of Copenhagen , Copenhagen DK-2200 , Denmark
| | - Xiang Zhang
- Beijing Advanced Innovation Center for Structural Biology, School of Medicine, School of Pharmaceutical Sciences , Tsinghua University , 100084 Beijing , China
| | - 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 79430 , United States
| | - Yang Du
- Department of Molecular and Cellular Physiology , Stanford University , Stanford , California 94305 , United States
| | - Cristina Cecchetti
- Department of Life Sciences , Imperial College London , London , SW7 2AZ , United Kingdom
| | - Weijiao Huang
- Department of Molecular and Cellular Physiology , Stanford University , Stanford , California 94305 , United States
| | - Hyoung Eun Bae
- Department of Bionanotechnology , Hanyang University , Ansan 155-88 , Korea
| | - Savvas Saouros
- Department of Life Sciences , Imperial College London , London , SW7 2AZ , United Kingdom
| | - Muhammad Ehsan
- Department of Bionanotechnology , Hanyang University , Ansan 155-88 , Korea
| | - 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 79430 , United States
| | - Xiangyu Liu
- Beijing Advanced Innovation Center for Structural Biology, School of Medicine, School of Pharmaceutical Sciences , Tsinghua University , 100084 Beijing , China
| | - Claus J Loland
- Department of Neuroscience , University of Copenhagen , Copenhagen DK-2200 , Denmark
| | - Brian K Kobilka
- Department of Molecular and Cellular Physiology , Stanford University , Stanford , California 94305 , United States
| | - Bernadette Byrne
- Department of Life Sciences , Imperial College London , London , SW7 2AZ , United Kingdom
| | - Pil Seok Chae
- Department of Bionanotechnology , Hanyang University , Ansan 155-88 , Korea
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27
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Sadaf A, Ramos M, Mortensen JS, Du Y, Bae HE, Munk CF, Hariharan P, Byrne B, Kobilka BK, Loland CJ, Guan L, Chae PS. Conformationally Restricted Monosaccharide-Cored Glycoside Amphiphiles: The Effect of Detergent Headgroup Variation on Membrane Protein Stability. ACS Chem Biol 2019; 14:1717-1726. [PMID: 31305987 DOI: 10.1021/acschembio.9b00166] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Detergents are widely used to isolate membrane proteins from lipid bilayers, but many proteins solubilized in conventional detergents are structurally unstable. Thus, there is major interest in the development of novel amphiphiles to facilitate membrane protein research. In this study, we have designed and synthesized novel amphiphiles with a rigid scyllo-inositol core, designated scyllo-inositol glycosides (SIGs). Varying the headgroup structure allowed the preparation of three sets of SIGs that were evaluated for their effects on membrane protein stability. When tested with a few model membrane proteins, representative SIGs conferred enhanced stability to the membrane proteins compared to a gold standard conventional detergent (DDM). Of the novel amphiphiles, a SIG designated STM-12 was most effective at preserving the stability of the multiple membrane proteins tested here. In addition, a comparative study of the three sets suggests that several factors, including micelle size and alkyl chain length, need to be considered in the development of novel detergents for membrane protein research. Thus, this study not only describes new detergent tools that are potentially useful for membrane protein structural study but also introduces plausible correlations between the chemical properties of detergents and membrane protein stabilization efficacy.
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Affiliation(s)
- Aiman Sadaf
- Department of Bionanotechnology, Hanyang University, Ansan 155-88, Korea
| | - Manuel Ramos
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States
| | - Jonas S. Mortensen
- Department of Neuroscience, University of Copenhagen, Copenhagen N DK-2200, Denmark
| | - Yang Du
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, California 94305, United States
| | - Hyoung Eun Bae
- Department of Bionanotechnology, Hanyang University, Ansan 155-88, Korea
| | - Chastine F. Munk
- Department of Neuroscience, University of Copenhagen, Copenhagen N DK-2200, Denmark
| | - 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 79430, United States
| | - Bernadette Byrne
- Department of Life Sciences, Imperial College London, London SW7 2AZ, U.K
| | - Brian K. Kobilka
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, California 94305, United States
| | - Claus J. Loland
- Department of Neuroscience, University of Copenhagen, Copenhagen N DK-2200, Denmark
| | - 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 79430, United States
| | - Pil Seok Chae
- Department of Bionanotechnology, Hanyang University, Ansan 155-88, Korea
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28
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Ehsan M, Du Y, Mortensen JS, Hariharan P, Qu Q, Ghani L, Das M, Grethen A, Byrne B, Skiniotis G, Keller S, Loland CJ, Guan L, Kobilka BK, Chae PS. Self-Assembly Behavior and Application of Terphenyl-Cored Trimaltosides for Membrane-Protein Studies: Impact of Detergent Hydrophobic Group Geometry on Protein Stability. Chemistry 2019; 25:11545-11554. [PMID: 31243822 DOI: 10.1002/chem.201902468] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Indexed: 01/13/2023]
Abstract
Amphipathic agents are widely used in various fields including biomedical sciences. Micelle-forming detergents are particularly useful for in vitro membrane-protein characterization. As many conventional detergents are limited in their ability to stabilize membrane proteins, it is necessary to develop novel detergents to facilitate membrane-protein research. In the current study, we developed novel trimaltoside detergents with an alkyl pendant-bearing terphenyl unit as a hydrophobic group, designated terphenyl-cored maltosides (TPMs). We found that the geometry of the detergent hydrophobic group substantially impacts detergent self-assembly behavior, as well as detergent efficacy for membrane-protein stabilization. TPM-Vs, with a bent terphenyl group, were superior to the linear counterparts (TPM-Ls) at stabilizing multiple membrane proteins. The favorable protein stabilization efficacy of these bent TPMs is likely associated with a binding mode with membrane proteins distinct from conventional detergents and facial amphiphiles. When compared to n-dodecyl-β-d-maltoside (DDM), most TPMs were superior or comparable to this gold standard detergent at stabilizing membrane proteins. Notably, TPM-L3 was particularly effective at stabilizing the human β2 adrenergic receptor (β2 AR), a G-protein coupled receptor, and its complex with Gs protein. Thus, the current study not only provides novel detergent tools that are useful for membrane-protein study, but also suggests a critical role for detergent hydrophobic group geometry in governing detergent efficacy.
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Affiliation(s)
- Muhammad Ehsan
- Department of Bionanotechnology, Hanyang University, Ansan, 15588, Korea.,Current address: Department of Chemistry, Mirpur University of Science & Technology, Mirpur, AJK, 10250, Pakistan)
| | - Yang Du
- Molecular and Cellular Physiology, Stanford, CA, 94305, USA
| | - Jonas S Mortensen
- Department of Neuroscience, University of Copenhagen, 2200, Copenhagen, Denmark
| | - 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
| | - Qianhui Qu
- Molecular and Cellular Physiology and Structural Biology, Stanford University, Stanford, CA, 94305, USA
| | - Lubna Ghani
- Department of Bionanotechnology, Hanyang University, Ansan, 15588, Korea
| | - Manabendra Das
- Molecular Biophysics, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 13, 67663, Kaiserslautern, Germany
| | - Anne Grethen
- Molecular Biophysics, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 13, 67663, Kaiserslautern, Germany
| | - Bernadette Byrne
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Georgios Skiniotis
- Molecular and Cellular Physiology and Structural Biology, Stanford University, Stanford, CA, 94305, USA
| | - Sandro Keller
- Molecular Biophysics, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 13, 67663, Kaiserslautern, Germany
| | - Claus J Loland
- Department of Neuroscience, University of Copenhagen, 2200, Copenhagen, Denmark
| | - 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
| | | | - Pil Seok Chae
- Department of Bionanotechnology, Hanyang University, Ansan, 15588, Korea
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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.
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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
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30
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Ehsan M, Du Y, Molist I, Seven AB, Hariharan P, Mortensen JS, Ghani L, Loland CJ, Skiniotis G, Guan L, Byrne B, Kobilka BK, Chae PS. Vitamin E-based glycoside amphiphiles for membrane protein structural studies. Org Biomol Chem 2019; 16:2489-2498. [PMID: 29564464 DOI: 10.1039/c8ob00270c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Membrane proteins play critical roles in a variety of cellular processes. For a detailed molecular level understanding of their biological functions and roles in disease, it is necessary to extract them from the native membranes. While the amphipathic nature of these bio-macromolecules presents technical challenges, amphiphilic assistants such as detergents serve as useful tools for membrane protein structural and functional studies. Conventional detergents are limited in their ability to maintain the structural integrity of membrane proteins and thus it is essential to develop novel agents with enhanced properties. Here, we designed and characterized a novel class of amphiphiles with vitamin E (i.e., α-tocopherol) as the hydrophobic tail group and saccharide units as the hydrophilic head group. Designated vitamin E-based glycosides (VEGs), these agents were evaluated for their ability to solubilize and stabilize a set of membrane proteins. VEG representatives not only conferred markedly enhanced stability to a diverse range of membrane proteins compared to conventional detergents, but VEG-3 also showed notable efficacy toward stabilization and visualization of a membrane protein complex. In addition to hydrophile-lipophile balance (HLB) of detergent molecules, the chain length and molecular geometry of the detergent hydrophobic group seem key factors in determining detergent efficacy for membrane protein (complex) stability.
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Affiliation(s)
- Muhammad Ehsan
- Department of Bionanotechnology, Hanyang University, Ansan, 15588, Korea.
| | - Yang Du
- Molecular and Cellular Physiology, Stanford, CA 94305, USA.
| | - Iago Molist
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK.
| | - Alpay B Seven
- Molecular and Cellular Physiology, 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.
| | - Jonas S Mortensen
- Department of Neuroscience, University of Copenhagen, DK- 2200 Copenhagen, Denmark.
| | - Lubna Ghani
- Department of Bionanotechnology, Hanyang University, Ansan, 15588, Korea.
| | - Claus J Loland
- Department of Neuroscience, University of Copenhagen, DK- 2200 Copenhagen, Denmark.
| | | | - 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.
| | - Bernadette Byrne
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK.
| | | | - Pil Seok Chae
- Department of Bionanotechnology, Hanyang University, Ansan, 15588, Korea.
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31
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Hussain H, Helton T, Du Y, Mortensen JS, Hariharan P, Ehsan M, Byrne B, Loland CJ, Kobilka BK, Guan L, Chae PS. A comparative study of branched and linear mannitol-based amphiphiles on membrane protein stability. Analyst 2019; 143:5702-5710. [PMID: 30334564 DOI: 10.1039/c8an01408f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The study of membrane proteins is extremely challenging, mainly because of the incompatibility of the hydrophobic surfaces of membrane proteins with an aqueous medium. Detergents are essential agents used to maintain membrane protein stability in non-native environments. However, conventional detergents fail to stabilize the native structures of many membrane proteins. Development of new amphipathic agents with enhanced efficacy for membrane protein stabilization is necessary to address this important problem. We have designed and synthesized linear and branched mannitol-based amphiphiles (MNAs), and comparative studies showed that most of the branched MNAs had advantages over the linear agents in terms of membrane protein stability. In addition, a couple of the new MNAs displayed favorable behaviors compared to n-dodecyl-β-d-maltoside and the previously developed MNAs in maintaining the native protein structures, indicating potential utility of these new agents in membrane protein study.
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Affiliation(s)
- Hazrat Hussain
- Department of Bionanotechnology, Hanyang University, Ansan, 15588, Korea.
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32
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Henderson RK, Fendler K, Poolman B. Coupling efficiency of secondary active transporters. Curr Opin Biotechnol 2018; 58:62-71. [PMID: 30502621 DOI: 10.1016/j.copbio.2018.11.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 11/14/2018] [Indexed: 10/27/2022]
Abstract
Secondary active transporters are fundamental to a myriad of biological processes. They use the electrochemical gradient of one solute to drive transport of another solute against its concentration gradient. Central to this mechanism is that the transport of one does not occur in the absence of the other. However, like in most of biology, imperfections in the coupling mechanism exist and we argue that these are innocuous and may even be beneficial for the cell. We discuss the energetics and kinetics of alternating-access in secondary transport and focus on the mechanistic aspects of imperfect coupling that give rise to leak pathways. Additionally, inspection of available transporter structures gives valuable insight into coupling mechanics, and we review literature where proteins have been altered to change their coupling efficiency.
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Affiliation(s)
- Ryan K Henderson
- Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Klaus Fendler
- Department of Biophysical Chemistry, Max-Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Bert Poolman
- Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
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33
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Bae HE, Du Y, Hariharan P, Mortensen JS, Kumar KK, Ha B, Das M, Lee HS, Loland CJ, Guan L, Kobilka BK, Chae PS. Asymmetric maltose neopentyl glycol amphiphiles for a membrane protein study: effect of detergent asymmetricity on protein stability. Chem Sci 2018; 10:1107-1116. [PMID: 30774908 PMCID: PMC6346398 DOI: 10.1039/c8sc02560f] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 11/04/2018] [Indexed: 12/21/2022] Open
Abstract
An asymmetric MNG, MNG-8,12, provided enhanced stability to human G protein-coupled receptors (GPCRs) compared to the symmetric MNG, MNG-3.
Maintaining protein stability in an aqueous solution is a prerequisite for protein structural and functional studies, but conventional detergents have increasingly showed limited ability to maintain protein integrity. A representative novel agent, maltose neopentyl glycol-3 (MNG-3), has recently substantially contributed to membrane protein structural studies. Motivated by the popular use of this novel agent, we prepared asymmetric versions of MNG-3 and evaluated these agents with several membrane proteins including two G protein-coupled receptors in this study. We found that some new MNGs were significantly more effective than MNG-3 at preserving protein integrity in the long term, suggesting that these asymmetric MNGs will find a wide use in membrane protein studies. In addition, this is the first study addressing the favorable effect of detergent asymmetric nature on membrane protein stability.
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Affiliation(s)
- Hyoung Eun Bae
- Department of Bionanotechnology , Hanyang University , Ansan , 15588 Korea .
| | - Yang Du
- Molecular and Cellular Physiology , 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 .
| | - Jonas S Mortensen
- Department of Neuroscience , University of Copenhagen , DK-2200 Copenhagen , Denmark .
| | - Kaavya K Kumar
- Molecular and Cellular Physiology , Stanford , CA 94305 , USA .
| | - Betty Ha
- Molecular and Cellular Physiology , Stanford , CA 94305 , USA .
| | - Manabendra Das
- Department of Bionanotechnology , Hanyang University , Ansan , 15588 Korea .
| | - Hyun Sung Lee
- Department of Bionanotechnology , Hanyang University , Ansan , 15588 Korea .
| | - Claus J Loland
- Department of Neuroscience , University of Copenhagen , DK-2200 Copenhagen , Denmark .
| | - 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 , CA 94305 , USA .
| | - Pil Seok Chae
- Department of Bionanotechnology , Hanyang University , Ansan , 15588 Korea .
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Das M, Du Y, Mortensen JS, Hariharan P, Lee HS, Byrne B, Loland CJ, Guan L, Kobilka BK, Chae PS. Rationally Engineered Tandem Facial Amphiphiles for Improved Membrane Protein Stabilization Efficacy. Chembiochem 2018; 19:2225-2232. [PMID: 30070754 DOI: 10.1002/cbic.201800388] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Indexed: 01/11/2023]
Abstract
A new family of tandem facial glucosides/maltosides (TFGs/TFMs) for membrane protein manipulation was prepared. The best detergent varied depending on the hydrophobic thickness of the target protein, but ether-based TFMs (TFM-C0E, TFM-C3E, and TFM-C5E) were notable for their ability to confer higher membrane protein stability than the previously developed amide-based TFA-1 (P. S. Chae, K. Gotfryd, J. Pacyna, L. J. W. Miercke, S. G. F. Rasmussen, R. A. Robbins, R. R. Rana, C. J. Loland, B. Kobilka, R. Stroud, B. Byrne, U. Gether, S. H. Gellman, J. Am. Chem. Soc. 2010, 132, 16750-16752). Thus, this study not only introduces novel agents with the potential to be used in membrane protein research but also highlights the importance of both the hydrophobic length and linker functionality of the detergent in stabilizing membrane proteins.
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Affiliation(s)
- Manabendra Das
- Department of Bionanotechnology, Hanyang University, 55 Hanyangdaehak-ro, Ansan, 155-88, Korea.,Present address: Molecular Biophysics, Technische Universität Kaiserslautern, Erwin-Schrödinger-Strasse 13, 67663, Kaiserslautern, Germany
| | - Yang Du
- Molecular and Cellular Physiology, Stanford University, 279 Campus Drive, Stanford, CA, 94305, USA
| | - Jonas S Mortensen
- Department of Neuroscience, University of Copenhagen, Blegdamsvej 3, 2200, Copenhagen, Denmark
| | - Parameswaran Hariharan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, 3601 4th St. MS 6551, Lubbock, TX, 79430, USA
| | - Hyun Sung Lee
- Department of Bionanotechnology, Hanyang University, 55 Hanyangdaehak-ro, Ansan, 155-88, Korea
| | - Bernadette Byrne
- Department of Life Sciences, Imperial College London, Exhibition Road, London, SW7 2AZ, UK
| | - Claus J Loland
- Department of Neuroscience, University of Copenhagen, Blegdamsvej 3, 2200, Copenhagen, Denmark
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, 3601 4th St. MS 6551, Lubbock, TX, 79430, USA
| | - Brian K Kobilka
- Molecular and Cellular Physiology, Stanford University, 279 Campus Drive, Stanford, CA, 94305, USA
| | - Pil Seok Chae
- Department of Bionanotechnology, Hanyang University, 55 Hanyangdaehak-ro, Ansan, 155-88, Korea
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35
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Hariharan P, Tikhonova E, Medeiros-Silva J, Jeucken A, Bogdanov MV, Dowhan W, Brouwers JF, Weingarth M, Guan L. Structural and functional characterization of protein-lipid interactions of the Salmonella typhimurium melibiose transporter MelB. BMC Biol 2018; 16:85. [PMID: 30075778 PMCID: PMC6091025 DOI: 10.1186/s12915-018-0553-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 07/23/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Membrane lipids play critical roles in the structure and function of membrane-embedded transporters. Salmonella typhimurium MelB (MelBSt) is a symporter coupling melibiose translocation with a cation (Na+, Li+, or H+). We present an extensive study on the effects of specific phospholipids on the structure of MelBSt and the melibiose transport catalyzed by this protein. RESULTS Lipidomic analysis and thin-layer chromatography (TLC) experiments reveal that at least one phosphatidylethanolamine (PE) and one phosphatidylglycerol (PG) molecule associate with MelBSt at high affinities. Solid-state nuclear magnetic resonance (ssNMR) spectroscopy experiments confirmed the presence of lipid tails and glycerol backbones that co-purified with MelBSt; headgroups of PG were also observed. Studies with lipid-engineered strains, including PE-deficient, cardiolipin (CL)- and PG-deficient, or CL-deficient strains, show that lack of PE or PG, however not CL, largely inhibits both H+- and Na+-coupled melibiose active transport to different extents. Interestingly, neither the co-substrate binding (melibiose or Na+) nor MelBSt folding and stability are affected by changing lipid compositions. Remarkably, the delipidated MelBSt with only 2-3 bound lipids, regardless of the headgroup species, also exhibits unchanged melting temperature values as shown by circular dichroism spectroscopy. CONCLUSIONS (1) Lipid tails and glycerol backbones of interacting PE and PG may contribute to the stability of the structure of MelBSt. (2) The headgroups of PE and PG, but not of CL, play important roles in melibiose transport; however, lipid headgroups do not modulate the folding and stability of MelBSt.
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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, 79430, 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, TX, 79430, USA
| | - João Medeiros-Silva
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Aike Jeucken
- Department of Biochemistry & Cell Biology, Lipidomics Facility, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 2, 3584 CM, Utrecht, The Netherlands
| | - Mikhail V Bogdanov
- Department of Biochemistry and Molecular Biology, the University of Texas Health Science, Center McGovern Medical School, Houston, TX, 77030, USA
| | - William Dowhan
- Department of Biochemistry and Molecular Biology, the University of Texas Health Science, Center McGovern Medical School, Houston, TX, 77030, USA
| | - Jos F Brouwers
- Department of Biochemistry & Cell Biology, Lipidomics Facility, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 2, 3584 CM, Utrecht, The Netherlands
| | - Markus Weingarth
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
| | - 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.
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36
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Ehsan M, Ghani L, Du Y, Hariharan P, Mortensen JS, Ribeiro O, Hu H, Skiniotis G, Loland CJ, Guan L, Kobilka BK, Byrne B, Chae PS. New penta-saccharide-bearing tripod amphiphiles for membrane protein structure studies. Analyst 2018; 142:3889-3898. [PMID: 28913526 DOI: 10.1039/c7an01168g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Integral membrane proteins either alone or as complexes carry out a range of key cellular functions. Detergents are indispensable tools in the isolation of membrane proteins from biological membranes for downstream studies. Although a large number of techniques and tools, including a wide variety of detergents, are available, purification and structural characterization of many membrane proteins remain challenging. In the current study, a new class of tripod amphiphiles bearing two different penta-saccharide head groups, designated TPSs, were developed and evaluated for their ability to extract and stabilize a range of diverse membrane proteins. Variations in the structures of the detergent head and tail groups allowed us to prepare three sets of the novel agents with distinctive structures. Some TPSs (TPS-A8 and TPS-E7) were efficient at extracting two proteins in a functional state while others (TPS-E8 and TPS-E10L) conferred marked stability to all membrane proteins (and membrane protein complexes) tested here compared to a conventional detergent. Use of TPS-E10L led to clear visualization of a receptor-Gs complex using electron microscopy, indicating profound potential in membrane protein research.
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Affiliation(s)
- Muhammad Ehsan
- Department of Bionanotechnology, Hanyang University, Ansan, 15588, Korea.
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37
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Ehsan M, Das M, Stern V, Du Y, Mortensen JS, Hariharan P, Byrne B, Loland CJ, Kobilka BK, Guan L, Chae PS. Steroid-Based Amphiphiles for Membrane Protein Study: The Importance of Alkyl Spacers for Protein Stability. Chembiochem 2018; 19:1433-1443. [PMID: 29660780 PMCID: PMC7238963 DOI: 10.1002/cbic.201800106] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Indexed: 01/04/2023]
Abstract
Membrane proteins allow effective communication between cells and organelles and their external environments. Maintaining membrane protein stability in a non-native environment is the major bottleneck to their structural study. Detergents are widely used to extract membrane proteins from the membrane and to keep the extracted protein in a stable state for downstream characterisation. In this study, three sets of steroid-based amphiphiles-glyco-diosgenin analogues (GDNs) and steroid-based pentasaccharides either lacking a linker (SPSs) or containing a linker (SPS-Ls)-have been developed as new chemical tools for membrane protein research. These detergents were tested with three membrane proteins in order to characterise their ability to extract membrane proteins from the membrane and to stabilise membrane proteins long-term. Some of the detergents, particularly the SPS-Ls, displayed favourable behaviour with the tested membrane proteins. This result indicates the potential utility of these detergents as chemical tools for membrane protein structural study and a critical role of the simple alkyl spacer in determining detergent efficacy.
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Affiliation(s)
- Muhammad Ehsan
- Department of Bionanotechnology, Hanyang University, 55 Hanyangdaehak-ro, Ansan, 15588, Republic of Korea
| | - Manabendra Das
- Department of Bionanotechnology, Hanyang University, 55 Hanyangdaehak-ro, Ansan, 15588, Republic of Korea
| | - Valerie Stern
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University, Health Sciences Center, 3601 4th Street, Lubbock, TX, 79430, USA
| | - Yang Du
- Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA, 94305, USA
| | - Jonas S Mortensen
- Department of Neuroscience, University of Copenhagen, Blegdamsvej 3, 2200, Copenhagen, Denmark
| | - Parameswaran Hariharan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University, Health Sciences Center, 3601 4th Street, Lubbock, TX, 79430, USA
| | - Bernadette Byrne
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Claus J Loland
- Department of Neuroscience, University of Copenhagen, Blegdamsvej 3, 2200, Copenhagen, Denmark
| | - Brian K Kobilka
- Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA, 94305, USA
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University, Health Sciences Center, 3601 4th Street, Lubbock, TX, 79430, USA
| | - Pil Seok Chae
- Department of Bionanotechnology, Hanyang University, 55 Hanyangdaehak-ro, Ansan, 15588, Republic of Korea
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38
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Sadaf A, Du Y, Santillan C, Mortensen JS, Molist I, Seven AB, Hariharan P, Skiniotis G, Loland CJ, Kobilka BK, Guan L, Byrne B, Chae PS. Dendronic trimaltoside amphiphiles (DTMs) for membrane protein study. Chem Sci 2017; 8:8315-8324. [PMID: 29619178 PMCID: PMC5858085 DOI: 10.1039/c7sc03700g] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 10/14/2017] [Indexed: 01/07/2023] Open
Abstract
A novel amphiphile with a dendronic hydrophobic group (DTM-A6) was markedly effective at stabilizing and visualizing a GPCR-Gs complex.
The critical contribution of membrane proteins in normal cellular function makes their detailed structure and functional analysis essential. Detergents, amphipathic agents with the ability to maintain membrane proteins in a soluble state in aqueous solution, have key roles in membrane protein manipulation. Structural and functional stability is a prerequisite for biophysical characterization. However, many conventional detergents are limited in their ability to stabilize membrane proteins, making development of novel detergents for membrane protein manipulation an important research area. The architecture of a detergent hydrophobic group, that directly interacts with the hydrophobic segment of membrane proteins, is a key factor in dictating their efficacy for both membrane protein solubilization and stabilization. In the current study, we developed two sets of maltoside-based detergents with four alkyl chains by introducing dendronic hydrophobic groups connected to a trimaltoside head group, designated dendronic trimaltosides (DTMs). Representative DTMs conferred enhanced stabilization to multiple membrane proteins compared to the benchmark conventional detergent, DDM. One DTM (i.e., DTM-A6) clearly outperformed DDM in stabilizing human β2 adrenergic receptor (β2AR) and its complex with Gs protein. A further evaluation of this DTM led to a clear visualization of β2AR-Gs complex via electron microscopic analysis. Thus, the current study not only provides novel detergent tools useful for membrane protein study, but also suggests that the dendronic architecture has a role in governing detergent efficacy for membrane protein stabilization.
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Affiliation(s)
- Aiman Sadaf
- Department of Bionanotechnology , Hanyang University , Ansan , 155-88 , Korea .
| | - Yang Du
- Molecular and Cellular Physiology , Stanford , CA 94305 , USA .
| | - Claudia Santillan
- 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 .
| | - Jonas S Mortensen
- Center of Neuroscience , University of Copenhagen , DK 2200 Copenhagen , Denmark .
| | - Iago Molist
- Department of Life Sciences , Imperial College London , London , SW7 2AZ , UK .
| | - Alpay B Seven
- Structural Biology & Molecular and Cellular Physiology , 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 .
| | - Georgios Skiniotis
- Structural Biology & Molecular and Cellular Physiology , Stanford , CA 94305 , USA .
| | - Claus J Loland
- Center of Neuroscience , University of Copenhagen , DK 2200 Copenhagen , Denmark .
| | - Brian K Kobilka
- Molecular and Cellular Physiology , Stanford , CA 94305 , USA .
| | - 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 .
| | - Bernadette Byrne
- Department of Life Sciences , Imperial College London , London , SW7 2AZ , UK .
| | - Pil Seok Chae
- Department of Bionanotechnology , Hanyang University , Ansan , 155-88 , Korea .
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Hariharan P, Guan L. Thermodynamic cooperativity of cosubstrate binding and cation selectivity of Salmonella typhimurium MelB. J Gen Physiol 2017; 149:1029-1039. [PMID: 29054867 PMCID: PMC5677108 DOI: 10.1085/jgp.201711788] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Revised: 08/17/2017] [Accepted: 09/13/2017] [Indexed: 12/20/2022] Open
Abstract
The melibiose symporter MelB couples melibiose transport to that of cations such as Na+. Hariharan and Guan show that the binding of Na+ and melibiose is thermodynamically cooperative and that Na+ coupling is based on ion concentrations and competitive binding, but not ion selectivity. The Na+-coupled melibiose symporter MelB, which can also be coupled to H+ or Li+ transport, is a prototype for the glycoside-pentoside-hexuronide:cation symporter family. Although the 3-D x-ray crystal structure of Salmonella typhimurium MelB (MelBSt) has been determined, the symport mechanisms for the obligatory coupled transport are not well understood. Here, we apply isothermal titration calorimetry to determine the energetics of Na+ and melibiose binding to MelBSt, as well as protonation of this transporter. Studies of the thermodynamic cycle for the formation of the Na+–MelBSt–melibiose ternary complex at pH 7.45 reveal that the binding of Na+ and melibiose is cooperative. The binding affinity for one substrate (Na+ or melibiose) is increased by the presence of the other by about eightfold. The coupling free energies (ΔΔG) of either substrate binding are ∼5 kJ/mol, and binding of both substrates releases a free energy of ∼35 kJ/mol. Measurements of the Na+-binding enthalpy at three different pH values, including the pKa value of MelB, indicate that the binding of one Na+ displaces one H+ per MelBSt molecule. In addition, the absolute dissociation constants for Na+ and H+, determined by competitive binding, show that MelBSt is selective for H+ over Na+ by ∼1,000-fold at a pKa of 6.25. Thus, the Na+ coupling in MelBSt is based not on ion selectivity but on ion concentrations and competitive binding because of a much higher Na+ concentration under physiological conditions. Such a selectivity feature seems to be common for membrane transport proteins that can bind both H+ and Na+ at a common site.
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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
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40
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Abstract
High-resolution membrane protein structures are essential for understanding the molecular basis of diverse biological events and important in drug development. Detergents are usually used to extract these bio-macromolecules from the membranes and maintain them in a soluble and stable state in aqueous solutions for downstream characterization. However, many eukaryotic membrane proteins solubilized in conventional detergents tend to undergo structural degradation, necessitating the development of new amphiphilic agents with enhanced properties. In this study, we designed and synthesized a novel class of glucoside amphiphiles, designated tandem malonate-based glucosides (TMGs). A few TMG agents proved effective at both stabilizing a range of membrane proteins and extracting proteins from the membrane environment. These favourable characteristics, along with synthetic convenience, indicate that these agents have potential in membrane protein research.
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41
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Hussain H, Du Y, Tikhonova E, Mortensen JS, Ribeiro O, Santillan C, Das M, Ehsan M, Loland CJ, Guan L, Kobilka BK, Byrne B, Chae PS. Resorcinarene-Based Facial Glycosides: Implication of Detergent Flexibility on Membrane-Protein Stability. Chemistry 2017; 23:6724-6729. [PMID: 28303608 DOI: 10.1002/chem.201605016] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Indexed: 11/08/2022]
Abstract
As a membrane-mimetic system, detergent micelles are popularly used to extract membrane proteins from lipid environments and to maintain their solubility and stability in an aqueous medium. However, many membrane proteins encapsulated in conventional detergents tend to undergo structural degradation during extraction and purification, thus necessitating the development of new agents with enhanced properties. In the current study, two classes of new amphiphiles are introduced, resorcinarene-based glucoside and maltoside amphiphiles (designated RGAs and RMAs, respectively), for which the alkyl chains are facially segregated from the carbohydrate head groups. Of these facial amphiphiles, two RGAs (RGA-C11 and RGA-C13) conferred markedly enhanced stability to four tested membrane proteins compared to a gold-standard conventional detergent. The relatively high water solubility and micellar stability of the RGAs compared to the RMAs, along with their generally favourable behaviours for membrane protein stabilisation described here, are likely to be, at least in part, a result of the high conformational flexibility of these glucosides. This study suggests that flexibility could be an important factor in determining the suitability of new detergents for membrane protein studies.
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Affiliation(s)
- Hazrat Hussain
- Department of Bionanotechnology, Hanyang University, Ansan, 155-88, Korea
| | - Yang Du
- Molecular and Cellular Physiology, Stanford University, Stanford, CA, 94305, 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, TX, 79430, USA
| | - Jonas S Mortensen
- Center of Neuroscience, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Orquidea Ribeiro
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Claudia Santillan
- 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
| | - Manabendra Das
- Department of Bionanotechnology, Hanyang University, Ansan, 155-88, Korea
| | - Muhammad Ehsan
- Department of Bionanotechnology, Hanyang University, Ansan, 155-88, Korea
| | - Claus J Loland
- Center of Neuroscience, University of Copenhagen, Copenhagen, 2200, Denmark
| | - 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
| | - Bernadette Byrne
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Pil Seok Chae
- Department of Bionanotechnology, Hanyang University, Ansan, 155-88, Korea
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42
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Das M, Du Y, Ribeiro O, Hariharan P, Mortensen JS, Patra D, Skiniotis G, Loland CJ, Guan L, Kobilka BK, Byrne B, Chae PS. Conformationally Preorganized Diastereomeric Norbornane-Based Maltosides for Membrane Protein Study: Implications of Detergent Kink for Micellar Properties. J Am Chem Soc 2017; 139:3072-3081. [PMID: 28218862 PMCID: PMC5818264 DOI: 10.1021/jacs.6b11997] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Detergents are essential tools for functional and structural studies of membrane proteins. However, conventional detergents are limited in their scope and utility, particularly for eukaryotic membrane proteins. Thus, there are major efforts to develop new amphipathic agents with enhanced properties. Here, a novel class of diastereomeric agents with a preorganized conformation, designated norbornane-based maltosides (NBMs), were prepared and evaluated for their ability to solubilize and stabilize membrane proteins. Representative NBMs displayed enhanced behaviors compared to n-dodecyl-β-d-maltoside (DDM) for all membrane proteins tested. Efficacy of the individual NBMs varied depending on the overall detergent shape and alkyl chain length. Specifically, NBMs with no kink in the lipophilic region conferred greater stability to the proteins than NBMs with a kink. In addition, long alkyl chain NBMs were generally better at stabilizing membrane proteins than short alkyl chain agents. Furthermore, use of one well-behaving NBM enabled us to attain a marked stabilization and clear visualization of a challenging membrane protein complex using electron microscopy. Thus, this study not only describes novel maltoside detergents with enhanced protein-stabilizing properties but also suggests that overall detergent geometry has an important role in determining membrane protein stability. Notably, this is the first systematic study on the effect of detergent kinking on micellar properties and associated membrane protein stability.
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Affiliation(s)
- Manabendra Das
- Department of Bionanotechnology, Hanyang University, Ansan 155-88, Korea
| | - Yang Du
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, California 94305, United States
| | - Orquidea Ribeiro
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - 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 79430, United States
| | - Jonas S. Mortensen
- Department of Neuroscience and Pharmacology, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Dhabaleswar Patra
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Georgios Skiniotis
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Claus J. Loland
- Department of Neuroscience and Pharmacology, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - 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 79430, United States
| | - Brian K. Kobilka
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, California 94305, United States
| | - Bernadette Byrne
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Pil Seok Chae
- Department of Bionanotechnology, Hanyang University, Ansan 155-88, Korea
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43
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Cho KH, Hariharan P, Mortensen JS, Du Y, Nielsen AK, Byrne B, Kobilka BK, Loland CJ, Guan L, Chae PS. Isomeric Detergent Comparison for Membrane Protein Stability: Importance of Inter-Alkyl-Chain Distance and Alkyl Chain Length. Chembiochem 2016; 17:2334-2339. [PMID: 27981750 DOI: 10.1002/cbic.201600429] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Indexed: 01/23/2023]
Abstract
Membrane proteins encapsulated by detergent micelles are widely used for structural study. Because of their amphipathic property, detergents have the ability to maintain protein solubility and stability in an aqueous medium. However, conventional detergents have serious limitations in their scope and utility, particularly for eukaryotic membrane proteins and membrane protein complexes. Thus, a number of new agents have been devised; some have made significant contributions to membrane protein structural studies. However, few detergent design principles are available. In this study, we prepared meta and ortho isomers of the previously reported para-substituted xylene-linked maltoside amphiphiles (XMAs), along with alkyl chain-length variation. The isomeric XMAs were assessed with three membrane proteins, and the meta isomer with a C12 alkyl chain was most effective at maintaining solubility/stability of the membrane proteins. We propose that interplay between the hydrophile-lipophile balance (HLB) and alkyl chain length is of central importance for high detergent efficacy. In addition, differences in inter-alkyl-chain distance between the isomers influence the ability of the detergents to stabilise membrane proteins.
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Affiliation(s)
- Kyung Ho Cho
- Department of Bionanotechnology, Hanyang University, 55 Hanyangdaehak-ro, Sangnok-gu, Ansan, 15588, Korea
| | - Parameswaran Hariharan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, 3601 4thStreet MS 6551, Lubbock, TX, 79430, USA
| | - Jonas S Mortensen
- Department of Neuroscience and Pharmacology, University of Copenhagen, Blegdamsvej 3, 18.6 Panum Institute, 2200, Copenhagen, Denmark
| | - Yang Du
- Molecular and Cellular Physiology, Stanford University, 157 Beckman Center, 279 Campus Drive, Stanford, CA, 94305, USA
| | - Anne K Nielsen
- Department of Neuroscience and Pharmacology, University of Copenhagen, Blegdamsvej 3, 18.6 Panum Institute, 2200, Copenhagen, Denmark
| | - Bernadette Byrne
- Department of Life Sciences, Imperial College London, Exhibition Road, South Kensington, London, SW7 2AZ, UK
| | - Brian K Kobilka
- Molecular and Cellular Physiology, Stanford University, 157 Beckman Center, 279 Campus Drive, Stanford, CA, 94305, USA
| | - Claus J Loland
- Department of Neuroscience and Pharmacology, University of Copenhagen, Blegdamsvej 3, 18.6 Panum Institute, 2200, Copenhagen, Denmark
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, 3601 4thStreet MS 6551, Lubbock, TX, 79430, USA
| | - Pil Seok Chae
- Department of Bionanotechnology, Hanyang University, 55 Hanyangdaehak-ro, Sangnok-gu, Ansan, 15588, Korea
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44
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Hariharan P, Andersson M, Jiang X, Pardon E, Steyaert J, Kaback HR, Guan L. Thermodynamics of Nanobody Binding to Lactose Permease. Biochemistry 2016; 55:5917-5926. [PMID: 27686537 DOI: 10.1021/acs.biochem.6b00826] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Camelid nanobodies (Nbs) raised against the outward-facing conformer of a double-Trp mutant of the lactose permease of Escherichia coli (LacY) stabilize the permease in outward-facing conformations. Isothermal titration calorimetry is applied herein to dissect the binding thermodynamics of two Nbs, one that markedly improves access to the sugar-binding site and another that dramatically increases the affinity for galactoside. The findings presented here show that both enthalpy and entropy contribute favorably to binding of the Nbs to wild-type (WT) LacY and that binding of Nb to double-Trp mutant G46W/G262W is driven by a greater enthalpy at an entropic penalty. Thermodynamic analyses support the interpretation that WT LacY is stabilized in outward-facing conformations like the double-Trp mutant with closure of the water-filled cytoplasmic cavity through conformational selection. The LacY conformational transition required for ligand binding is reflected by a favorable entropy increase. Molecular dynamics simulations further suggest that the entropy increase likely stems from release of immobilized water molecules primarily from the cytoplasmic cavity upon closure.
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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, Texas 79430, United States
| | - Magnus Andersson
- Department of Theoretical Physics and Swedish e-Science Research Center, Science for Life Laboratory, KTH Royal Institute of Technology , SE-171 21 Solna, Sweden
| | - Xiaoxu Jiang
- Department of Physiology, University of California , Los Angeles, California 90095, United States
| | - Els Pardon
- VIB Center for Structural Biology Research, VIB , 1050 Brussel, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel , Pleinlaan 2, 1050 Brussel, Belgium
| | - Jan Steyaert
- VIB Center for Structural Biology Research, VIB , 1050 Brussel, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel , Pleinlaan 2, 1050 Brussel, Belgium
| | - H Ronald Kaback
- Department of Physiology, University of California , Los Angeles, California 90095, United States
| | - 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 79430, United States
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45
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Katsube S, Sato K, Ando T, Isogai E, Yoneyama H. Secretion of d-alanine by Escherichia coli. Microbiology (Reading) 2016; 162:1243-1252. [DOI: 10.1099/mic.0.000305] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Affiliation(s)
- Satoshi Katsube
- Laboratory of Animal Microbiology, Department of Microbial Biotechnology, Graduate School of Agricultural Science, Tohoku University, 1-1, Amamiya-machi, Tsutsumidori, Aoba-ku, Sendai 981-8555, Japan
| | - Kazuki Sato
- Laboratory of Animal Microbiology, Department of Microbial Biotechnology, Graduate School of Agricultural Science, Tohoku University, 1-1, Amamiya-machi, Tsutsumidori, Aoba-ku, Sendai 981-8555, Japan
| | - Tasuke Ando
- Laboratory of Animal Microbiology, Department of Microbial Biotechnology, Graduate School of Agricultural Science, Tohoku University, 1-1, Amamiya-machi, Tsutsumidori, Aoba-ku, Sendai 981-8555, Japan
| | - Emiko Isogai
- Laboratory of Animal Microbiology, Department of Microbial Biotechnology, Graduate School of Agricultural Science, Tohoku University, 1-1, Amamiya-machi, Tsutsumidori, Aoba-ku, Sendai 981-8555, Japan
| | - Hiroshi Yoneyama
- Laboratory of Animal Microbiology, Department of Microbial Biotechnology, Graduate School of Agricultural Science, Tohoku University, 1-1, Amamiya-machi, Tsutsumidori, Aoba-ku, Sendai 981-8555, Japan
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46
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Ehsan M, Du Y, Scull NJ, Tikhonova E, Tarrasch J, Mortensen JS, Loland CJ, Skiniotis G, Guan L, Byrne B, Kobilka BK, Chae PS. Highly Branched Pentasaccharide-Bearing Amphiphiles for Membrane Protein Studies. J Am Chem Soc 2016; 138:3789-96. [PMID: 26966956 DOI: 10.1021/jacs.5b13233] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Detergents are essential tools for membrane protein manipulation. Micelles formed by detergent molecules have the ability to encapsulate the hydrophobic domains of membrane proteins. The resulting protein-detergent complexes (PDCs) are compatible with the polar environments of aqueous media, making structural and functional analysis feasible. Although a number of novel agents have been developed to overcome the limitations of conventional detergents, most have traditional head groups such as glucoside or maltoside. In this study, we introduce a class of amphiphiles, the PSA/Es with a novel highly branched pentasaccharide hydrophilic group. The PSA/Es conferred markedly increased stability to a diverse range of membrane proteins compared to conventional detergents, indicating a positive role for the new hydrophilic group in maintaining the native protein integrity. In addition, PDCs formed by PSA/Es were smaller and more suitable for electron microscopic analysis than those formed by DDM, indicating that the new agents have significant potential for the structure-function studies of membrane proteins.
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Affiliation(s)
- Muhammad Ehsan
- Department of Bionanotechnology, Hanyang University , Ansan, 426-791, Korea
| | - Yang Du
- Molecular and Cellular Physiology, Stanford University , Stanford, California 94305, United States
| | - Nicola J Scull
- Department of Life Sciences, Imperial College London , London, SW7 2AZ, U.K
| | - 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 79430, United States
| | - Jeffrey Tarrasch
- Life Sciences Institute, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Jonas S Mortensen
- Department of Neuroscience and Pharmacology, University of Copenhagen , Copenhagen, DK-2200, Denmark
| | - Claus J Loland
- Department of Neuroscience and Pharmacology, University of Copenhagen , Copenhagen, DK-2200, Denmark
| | - Georgios Skiniotis
- Life Sciences Institute, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - 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 79430, United States
| | - Bernadette Byrne
- Department of Life Sciences, Imperial College London , London, SW7 2AZ, U.K
| | - Brian K Kobilka
- Molecular and Cellular Physiology, Stanford University , Stanford, California 94305, United States
| | - Pil Seok Chae
- Department of Bionanotechnology, Hanyang University , Ansan, 426-791, Korea
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47
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Sadaf A, Mortensen JS, Capaldi S, Tikhonova E, Hariharan P, de Castro Ribeiro O, Loland CJ, Guan L, Byrne B, Chae PS. A Class of Rigid Linker-bearing Glucosides for Membrane Protein Structural Study. Chem Sci 2015; 7:1933-1939. [PMID: 27110345 PMCID: PMC4836865 DOI: 10.1039/c5sc02900g] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Novel glycoside amphiphile (NDT-C11) displays favorable behavior in maintaining both protein stability and conformational flexibility compared to DDM and MNG-3.
Membrane proteins are amphipathic bio-macromolecules incompatible with the polar environments of aqueous media. Conventional detergents encapsulate the hydrophobic surfaces of membrane proteins allowing them to exist in aqueous solution. Membrane proteins stabilized by detergent micelles are used for structural and functional analysis. Despite the availability of a large number of detergents, only a few agents are sufficiently effective at maintaining the integrity of membrane proteins to allow successful crystallization. In the present study, we describe a novel class of synthetic amphiphiles with a branched tail group and a triglucoside head group. These head and tail groups were connected via an amide or ether linkage by using a tris(hydroxylmethyl)aminomethane (TRIS) or neopentyl glycol (NPG) linker to produce TRIS-derived triglucosides (TDTs) and NPG-derived triglucosides (NDTs), respectively. Members of this class conferred enhanced stability on target membrane proteins compared to conventional detergents. Because of straightforward synthesis of the novel agents and their favourable effects on a range of membrane proteins, these agents should be of wide applicability to membrane protein science.
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Affiliation(s)
- Aiman Sadaf
- Department of Bionanotechnology, Hanyang University, Ansan, 426-791 (Korea)
| | - Jonas S Mortensen
- Department of Neuroscience and Pharmacology, University of Copenhagen, DK-2200 Copenhagen (Denmark)
| | - Stefano Capaldi
- Department of Life Sciences, Imperial College London London, SW7 2AZ (UK) ; Department of Biotechnology, University of Verona, 37134 Verona (Italy)
| | - Elena Tikhonova
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences
| | - Parameswaran Hariharan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences
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48
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Amin A, Hariharan P, Chae PS, Guan L. Effect of Detergents on Galactoside Binding by Melibiose Permeases. Biochemistry 2015; 54:5849-55. [PMID: 26352464 DOI: 10.1021/acs.biochem.5b00660] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The effect of various detergents on the stability and function of the melibiose permeases of Escherichia coli (MelBEc) and Salmonella typhimurium (MelBSt) was studied. In n-dodecyl-β-d-maltoside (DDM) or n-undecyl-β-d-maltoside (UDM), WT MelBSt binds melibiose with an affinity similar to that in the membrane. However, with WT MelBEc or MelBSt mutants (Arg141 → Cys, Arg295 → Cys, or Arg363 → Cys), galactoside binding is not detected in these detergents, but binding to the phosphotransferase protein IIA(Glc) is maintained. In the amphiphiles lauryl maltose neopentyl glycol (MNG-3) or glyco-diosgenin (GDN), galactoside binding with all of the MelB proteins is observed, with slightly reduced affinities. MelBSt is more thermostable than MelBEc, and the thermostability of either MelB is largely increased in MNG-3 or GDN. Therefore, the functional defect with DDM or UDM likely results from the relative instability of the sensitive MelB proteins, and stability, as well as galactoside binding, is retained in MNG-3 or GDN. Furthermore, isothermal titration calorimetry of melibiose binding with MelBSt shows that the favorable entropic contribution to the binding free energy is decreased in MNG-3, indicating that the conformational dynamics of MelB is restricted in this detergent.
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Affiliation(s)
- Anowarul Amin
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center , Lubbock, Texas 79430, United States
| | - 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 79430, United States
| | - Pil Seok Chae
- Department of Bionanotechnology, Hanyang University , Ansan 426-791, Korea
| | - 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 79430, United States
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49
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Kuang Q, Purhonen P, Pattipaka T, Ayele YH, Hebert H, Koeck PJB. A Refined Single-Particle Reconstruction Procedure to Process Two-Dimensional Crystal Images from Transmission Electron Microscopy. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2015; 21:876-885. [PMID: 25990985 DOI: 10.1017/s1431927615000616] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Single-particle reconstruction (SPR) and electron crystallography (EC), two major applications in electron microscopy, can be used to determine the structure of membrane proteins. The three-dimensional (3D) map is obtained from separated particles in conventional SPR, but from periodic unit cells in EC. Here, we report a refined SPR procedure for processing 2D crystal images. The method is applied to 2D crystals of melibiose permease, a secondary transporter in Escherichia coli. The current procedure is improved from our previously published one in several aspects. The "gold standard Fourier shell correlation" resolution of our final reconstruction reaches 13 Å, which is significantly better than the previously obtained 17 Å resolution. The choices of different refinement parameters for reconstruction are discussed. Our refined SPR procedure could be applied to determine the structure of other membrane proteins in small or locally distorted 2D crystals, which are not ideal for EC.
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Affiliation(s)
- Qie Kuang
- Karolinska Institutet,Department of Biosciences and Nutrition and KTH Royal Institute of Technology,School of Technology and Health,Novum,S-14183 Huddinge,Sweden
| | - Pasi Purhonen
- Karolinska Institutet,Department of Biosciences and Nutrition and KTH Royal Institute of Technology,School of Technology and Health,Novum,S-14183 Huddinge,Sweden
| | - Thirupathi Pattipaka
- Karolinska Institutet,Department of Biosciences and Nutrition and KTH Royal Institute of Technology,School of Technology and Health,Novum,S-14183 Huddinge,Sweden
| | - Yohannes H Ayele
- Karolinska Institutet,Department of Biosciences and Nutrition and KTH Royal Institute of Technology,School of Technology and Health,Novum,S-14183 Huddinge,Sweden
| | - Hans Hebert
- Karolinska Institutet,Department of Biosciences and Nutrition and KTH Royal Institute of Technology,School of Technology and Health,Novum,S-14183 Huddinge,Sweden
| | - Philip J B Koeck
- Karolinska Institutet,Department of Biosciences and Nutrition and KTH Royal Institute of Technology,School of Technology and Health,Novum,S-14183 Huddinge,Sweden
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50
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Cho KH, Du Y, Scull NJ, Hariharan P, Gotfryd K, Loland CJ, Guan L, Byrne B, Kobilka BK, Chae PS. Novel Xylene-Linked Maltoside Amphiphiles (XMAs) for Membrane Protein Stabilisation. Chemistry 2015; 21:10008-13. [PMID: 26013293 DOI: 10.1002/chem.201501083] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Indexed: 01/14/2023]
Abstract
Membrane proteins are key functional players in biological systems. These biomacromolecules contain both hydrophilic and hydrophobic regions and thus amphipathic molecules are necessary to extract membrane proteins from their native lipid environments and stabilise them in aqueous solutions. Conventional detergents are commonly used for membrane protein manipulation, but membrane proteins surrounded by these agents often undergo denaturation and aggregation. In this study, a novel class of maltoside-bearing amphiphiles, with a xylene linker in the central region, designated xylene-linked maltoside amphiphiles (XMAs) was developed. When these novel agents were evaluated with a number of membrane proteins, it was found that XMA-4 and XMA-5 have particularly favourable efficacy with respect to membrane protein stabilisation, indicating that these agents hold significant potential for membrane protein structural study.
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Affiliation(s)
- Kyung Ho Cho
- Department of Bionanotechnology, Hanyang University, Ansan, 426-791 (Republic of Korea)
| | - Yang Du
- Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305 (USA)
| | - Nicola J Scull
- Department of Life Sciences, Imperial College London, London, SW7 2AZ (UK)
| | - 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)
| | - Kamil Gotfryd
- Department of Neuroscience and Pharmacology, University of Copenhagen, 2200 Copenhagen (Denmark).,Present address: Department of Biomedical Sciences, University of Copenhagen, 2200 Copenhagen (Denmark)
| | - Claus J Loland
- Department of Neuroscience and Pharmacology, University of Copenhagen, 2200 Copenhagen (Denmark)
| | - 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)
| | - Bernadette Byrne
- Department of Life Sciences, Imperial College London, London, SW7 2AZ (UK)
| | - Brian K Kobilka
- Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305 (USA)
| | - Pil Seok Chae
- Department of Bionanotechnology, Hanyang University, Ansan, 426-791 (Republic of Korea).
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