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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Nanatani K, Ishii T, Masuda A, Katsube S, Ando T, Yoneyama H, Abe K. Novel transporter screening technology for chemical production by microbial fermentation. J GEN APPL MICROBIOL 2023; 69:142-149. [PMID: 36567121 DOI: 10.2323/jgam.2022.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
In the fermentative production of compounds by using microorganisms, control of the transporter activity responsible for substrate uptake and product efflux, in addition to intracellular metabolic modification, is important from a productivity perspective. However, there has been little progress in analyses of the functions of microbial membrane transporters, and because of the difficulty in finding transporters that transport target compounds, only a few transporters have been put to practical use. Here, we constructed a Corynebacterium glutamicum-derived transporter expression library (CgTP-Express library) with the fusion partner gene mstX and used a peptide-feeding method with the dipeptide L-Ala-L-Ala to search for alanine exporters in the library. Among 39 genes in the library, five candidate alanine exporters (NCgl2533, NCgl2683, NCgl0986, NCgl0453, and NCgl0929) were found; expression of NCgl2533 increased the alanine concentration in cell culture. The CgTP-Express library was thus effective for finding a new transporter candidate.
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Affiliation(s)
- Kei Nanatani
- Department of Microbial Resources, Graduate School of Agricultural Science, Tohoku University
- Laboratory of Applied Microbiology, Department of Microbial Biotechnology, Graduate School of Agricultural Science, Tohoku University
- The Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University
- Tohoku Medical Megabank Organization, Tohoku University
| | - Tomoko Ishii
- Laboratory of Applied Microbiology, Department of Microbial Biotechnology, Graduate School of Agricultural Science, Tohoku University
| | - Ayumu Masuda
- Laboratory of Applied Microbiology, Department of Microbial Biotechnology, Graduate School of Agricultural Science, Tohoku University
| | - Satoshi Katsube
- Laboratory of Animal Microbiology, Department of Microbial Biotechnology, Graduate School of Agricultural Science, Tohoku University
| | - Tasuke Ando
- Laboratory of Animal Microbiology, Department of Microbial Biotechnology, Graduate School of Agricultural Science, Tohoku University
| | - Hiroshi Yoneyama
- Laboratory of Animal Microbiology, Department of Microbial Biotechnology, Graduate School of Agricultural Science, Tohoku University
| | - Keietsu Abe
- Department of Microbial Resources, Graduate School of Agricultural Science, Tohoku University
- Laboratory of Applied Microbiology, Department of Microbial Biotechnology, Graduate School of Agricultural Science, Tohoku University
- Microbial Genomics Laboratory, New Industry Creation Hatchery Center, Tohoku University
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3
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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 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] [What about the content of this article? (0)] [Affiliation(s)] [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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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8
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Ghani L, Kim S, Wang H, Lee HS, Mortensen JS, Katsube S, Du Y, Sadaf A, Ahmed W, Byrne B, Guan L, Loland CJ, Kobilka BK, Im W, Chae PS. Foldable Detergents for Membrane Protein Study: Importance of Detergent Core Flexibility in Protein Stabilization. Chemistry 2022; 28:e202200116. [PMID: 35238091 PMCID: PMC9007890 DOI: 10.1002/chem.202200116] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Indexed: 12/30/2022]
Abstract
Membrane proteins are of biological and pharmaceutical significance. However, their structural study is extremely challenging mainly due to the fact that only a small number of chemical tools are suitable for stabilizing membrane proteins in solution. Detergents are widely used in membrane protein study, but conventional detergents are generally poor at stabilizing challenging membrane proteins such as G protein-coupled receptors and protein complexes. In the current study, we prepared tandem triazine-based maltosides (TZMs) with two amphiphilic triazine units connected by different diamine linkers, hydrazine (TZM-Hs) and 1,2-ethylenediamine (TZM-Es). These TZMs were consistently superior to a gold standard detergent (DDM) in terms of stabilizing a few membrane proteins. In addition, the TZM-Es containing a long linker showed more general protein stabilization efficacy with multiple membrane proteins than the TZM-Hs containing a short linker. This result indicates that introduction of the flexible1,2-ethylenediamine linker between two rigid triazine rings enables the TZM-Es to fold into favourable conformations in order to promote membrane protein stability. The novel concept of detergent foldability introduced in the current study has potential in rational detergent design and membrane protein applications.
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Affiliation(s)
- Lubna Ghani
- Department of Bionano Engineering, Center for Bionano Intelligence Education and Research, Hanyang University, Ansan, 155-88, South Korea
| | - Seonghoon Kim
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul, 024-55, South Korea
| | - Haoqing Wang
- Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
| | - Hyun Sung Lee
- Department of Bionano Engineering, Center for Bionano Intelligence Education and Research, Hanyang University, Ansan, 155-88, South Korea
| | - Jonas S Mortensen
- Department of Neuroscience, University of Copenhagen, Copenhagen, 2200, Denmark
| | - 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
| | - Yang Du
- Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA.,Current address: School of Life and Health Sciences, Chinese University of Hong Kong, 2001 Longxiang Ave, Shenzhen, Guangdong, 518172, China
| | - Aiman Sadaf
- Department of Bionano Engineering, Center for Bionano Intelligence Education and Research, Hanyang University, Ansan, 155-88, South Korea
| | - Waqar Ahmed
- Department of Bionano Engineering, Center for Bionano Intelligence Education and Research, Hanyang University, Ansan, 155-88, South Korea
| | - 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
| | - Claus J Loland
- Department of Neuroscience, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Brian K Kobilka
- Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
| | - Wonpil Im
- Department of Biological Sciences, Chemistry, and Bioengineering, Lehigh University, Bethlehem, PA 18015, USA
| | - 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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9
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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] [What about the content of this article? (0)] [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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10
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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11
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Katsube S, Liang R, Amin A, Hamuli B, Parameswaran H, Guan L. Metal selectivity in the Salmonella typhimurium melibiose permease MelB. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.1508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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12
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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13
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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 DOI: 10.1016/j.actbio.2020.06.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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14
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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15
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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16
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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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17
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Zhao J, Katsube S, Yamamoto J, Yamasaki K, Miyagishi M, Iwai S. Analysis of ATP and AMP binding to a DNA aptamer and its imidazole-tethered derivatives by surface plasmon resonance. Analyst 2015. [PMID: 26221631 DOI: 10.1039/c5an01347j] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Imidazole was tethered to the C5 position of thymine in an ATP-binding DNA aptamer with two types of linkers, and the affinities of each aptamer for ATP and AMP were determined by surface plasmon resonance measurements. The imidazole-tethered aptamers exhibited higher affinity for ATP, almost independently of the linker structure or the modification site.
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Affiliation(s)
- Jing Zhao
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
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18
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Kim S, Ihara K, Katsube S, Hori H, Ando T, Isogai E, Yoneyama H. Characterization of the l-alanine exporter AlaE of Escherichia coli and its potential role in protecting cells from a toxic-level accumulation of l-alanine and its derivatives. Microbiologyopen 2015; 4:632-43. [PMID: 26073055 PMCID: PMC4554458 DOI: 10.1002/mbo3.269] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 04/21/2015] [Accepted: 05/04/2015] [Indexed: 11/14/2022] Open
Abstract
We previously reported that the alaE gene of Escherichia coli encodes the l-alanine exporter AlaE. The objective of this study was to elucidate the mechanism of the AlaE exporter. The minimum inhibitory concentration of l-alanine and l-alanyl-l-alanine in alaE-deficient l-alanine-nonmetabolizing cells MLA301ΔalaE was 4- and >4000-fold lower, respectively, than in the alaE-positive parent cells MLA301, suggesting that AlaE functions as an efflux pump to avoid a toxic-level accumulation of intracellular l-alanine and its derivatives. Furthermore, the growth of the alaE-deficient mutant derived from the l-alanine-metabolizing strain was strongly inhibited in the presence of a physiological level of l-alanyl-l-alanine. Intact MLA301ΔalaE and MLA301ΔalaE/pAlaE cells producing plasmid-borne AlaE, accumulated approximately 200% and 50%, respectively, of the [3H]l-alanine detected in MLA301 cells, suggesting that AlaE exports l-alanine. When 200 mmol/L l-alanine-loaded inverted membrane vesicles prepared from MLA301ΔalaE/pAlaE were placed in a solution containing 200 mmol/L or 0.34 μmol/L l-alanine, energy-dependent [3H]l-alanine accumulation occurred under either condition. This energy-dependent uphill accumulation of [3H]l-alanine was strongly inhibited in the presence of carbonyl cyanide m-chlorophenylhydrazone but not by dicyclohexylcarbodiimide, suggesting that the AlaE-mediated l-alanine extrusion was driven by proton motive force. Based on these results, physiological roles of the l-alanine exporter are discussed.
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Affiliation(s)
- Seryoung Kim
- 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
| | - Kohei Ihara
- 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
| | - 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
| | - Hatsuhiro Hori
- 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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19
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Obayashi O, Sasaki S, Katsube S, Uta S, Kaneko K, Yanagihara Y. The relationship between postoperative results and bone dynamics in RA patients who underwent cementless Ortholoc II TKA: histomorphometric study. Mod Rheumatol 2000. [DOI: 10.1007/s101650050005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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20
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Obayashi O, Sasaki S, Katsube S, Uta S, Kaneko K, Yanagihara Y. The relationship between postoperative results and bone dynamics in RA patients who underwent cementless Ortholoc II TKA: histomorphometric study. Mod Rheumatol 2000; 10:88-94. [PMID: 24383562 DOI: 10.3109/s101650050005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract We previously reported a histomorphometric study of iliac bone obtained at the time of cementless total knee arthroplasty (TKA) in patients with rheumatoid arthritis (RA). In this paper, we further extended our analysis to investigate the postoperative results and radiographs after TKA in association with bone metabolism. All the patients were female, ranging in age from 38 to 68 years (mean, 56.8 years). Histomorphometric results demonstrated that bone volume and trabecular thickness were decreased, whereas bone absorption and bone formation rate (BFR) were increased. The bone in patients with mutilating disease (MUD) showed remarkably increased bone turnover and osteoporosis compared with those of the more erosive subset (MES) patients. Sixteen out of the 20 patients were alive at the time of follow-up (follow-up period between 5 years 10 months and 8 years 11 months). Among them, 10 patients could be further examined. Radiolucent lines (RLL) were assessed by the modified Knee Society evaluation (scoring) system. The number of RLL (N-RLL) were correlated with BFR in morphometric examination. In addition, the weight-bearing zones in the N-RLL were more significantly correlated with BFR. The Japanese Orthopedic Association (JOA) score and pain score negatively correlated with eroded bone surface. The present study indicated that bone dynamics, rather than the bone volume at the time of TKA, were involved in the presence of RLL and in pain after surgery for TKA.
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Affiliation(s)
- O Obayashi
- Department of Orthopedic Surgery, Juntendo University School of Medicine , Tokyo , Japan
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21
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Rao S, Shirata K, Furukawa KS, Ushida T, Tateishi T, Kanazawa M, Katsube S, Janna S. Evaluation of cytotoxicity of UHMWPE wear debris. Biomed Mater Eng 2000; 9:209-17. [PMID: 10674175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
We established a novel method to investigate the phagocytosis of ultra high molecular weight polyethylene using primary macrophage cells by an inverted cell culture method. Abundant wear debris derived from implant materials are generated in aseptic loosening and are deposited in periprosthetic tissues in which they are phagocytized by mono- and multi-nucleated macrophage like cells. Ultra-high-molecular-weight-polyethylene wear debris generated from different sources namely, from laboratory test wear machine, in vivo methods and from knee and hip simulator were mainly used in this investigation. The cytotoxicity index of the different UHMWPE particles obtained from various sources were compared with that of the PE beads and the control without particles by Alamar Blue and Neutral Red assays. The results showed that the cytotoxicity index was significantly lower for the wear debris from the in vivo experiments than that for other particles. SEM analysis were also done to understand the morphology of the wear debris and polyethylene beads and to confirm the phagocytosis process. The mean diameter of the wear debris obtained from the in vivo experiments as estimated from the imaging analysis of the SEM photographs was found to be the least. The inverted cell culture method may be regarded as one of the good methods to study the phagocytosis of UHMWPE by macrophage cells.
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Affiliation(s)
- S Rao
- National Institute for Advanced Interdisciplinary Research, Tsukuba, Japan
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Amano A, Miyagi K, Azuma T, Ishihara Y, Katsube S, Aoyama I, Saito I. Histological studies on the rheumatoid synovial membrane irradiated with a low energy laser. Lasers Surg Med 1994; 15:290-4. [PMID: 7830475 DOI: 10.1002/lsm.1900150309] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The beneficial effects of low energy laser irradiation on rheumatoid arthritis (RA) joints have been reported, but the mechanisms of action of low energy lasers in RA are unclear. The synovial membrane in cases of RA was studied histologically to observe the effects of low energy laser irradiation. Fourteen knee joints of RA cases, which had been scheduled for arthroplasty, were irradiated with a gallium-aluminium-arsenide (Ga-Al-As) laser (790 nm in wavelength and 10 mW of output power) prior to the surgical operation, at six points of the external aspect of the knee joint for 80 seconds at each points once a day for 6 days. On the day following the last irradiation, pieces of synovial membrane from the lateral irradiated area and from the median nonirradiated area as a control were resected during the arthroplasty. The histological findings of the irradiated synovial membrane showed flattening of epithelial cells, decreased villous proliferation, narrowed vascular lumen, and less infiltration of inflammatory cells compared with those of nonirradiated synovia. The evaluation of slides was done in a blinded manner, and significant differences was seen by Wilcoxon's t-test (P < 0.01). Histological findings suggested that the low energy laser irradiation induced suppression of inflammation in the synovial membrane of RA.
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Affiliation(s)
- A Amano
- Department of Internal Medicine, Toyoko Hospital, St. Marianna University, Kanagawa, Japan
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Katsube S. [Roentgenological and histopathological studies of the hip joint in rheumatoid arthritis]. Nihon Seikeigeka Gakkai Zasshi 1990; 64:378-91. [PMID: 2380592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In order to study the disease process of the hip joint in rheumatoid arthritis, roentgenological analysis was carried out along with histological studies on the resected femoral heads. For the roentgenological study, hip roentgenograms of seven patients with known natural course and sixty preoperative patients were used. For the histological study, sixteen resected femoral heads affected by various disease types were used. The histological findings were compared with the roentgenological findings. As specific roentgenological findings, there were osteoporosis, burrowing and inward protrusion of the acetabulum, and collapse and flattening of the femoral head. A sequential process of the femoral head destruction was demonstrated, starting from collapse, through flattening, and finally ending in disappearance. The collapse was divided into sclerotic collapse and porotic collapse, and their roentgenological and histological differences were discussed. In addition to the common destruction process, the presence of the following three uncommon types was suggested for a better understanding of clinical manifestations: stiff type (4.5%), synovial proliferation type (6.0%) and aseptic necrosis type (3.0%).
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Affiliation(s)
- S Katsube
- Department of Orthopaedic Surgery, Juntendo University, School of Medicine, Tokyo, Japan
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Sawa Y, Hattori T, Kawakami Y, Katsube S, Goto A. [Synthesis of 6-chloro-5-CYClohexyl-1-indancarboxylic acid and related compounds]. YAKUGAKU ZASSHI 1976; 96:653-8. [PMID: 1085819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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