1
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Wu H, Tan Y, Ngai WL, Li X. Total synthesis of interleukin-2 via a tunable backbone modification strategy. Chem Sci 2023; 14:1582-1589. [PMID: 36794182 PMCID: PMC9906654 DOI: 10.1039/d2sc05660g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 01/06/2023] [Indexed: 01/08/2023] Open
Abstract
Chemical synthesis of hydrophobic proteins presents a formidable task as they are often difficultly achieved via peptide synthesis, purification, and peptide ligation. Thus, peptide solubilizing strategies are needed to integrate with peptide ligation to achieve protein total synthesis. Herein, we report a tunable backbone modification strategy, taking advantage of the tunable stability of the Cys/Pen ligation intermediate, which allows for readily introducing a solubilizing tag for both peptide purification and ligation processes. The effectiveness of this strategy was demonstrated by the chemical synthesis of interleukin-2.
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Affiliation(s)
- Hongxiang Wu
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong Hong Kong SAR P. R. China
| | - Yi Tan
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong Hong Kong SAR P. R. China
| | - Wai Lok Ngai
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong Hong Kong SAR P. R. China
| | - Xuechen Li
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong Hong Kong SAR P. R. China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology Qingdao 266237 P. R. China
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2
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Baumruck AC, Yang J, Thomas GF, Beyer LI, Tietze D, Tietze AA. Native Chemical Ligation of Highly Hydrophobic Peptides in Ionic Liquid-Containing Media. J Org Chem 2021; 86:1659-1666. [PMID: 33400874 PMCID: PMC7886022 DOI: 10.1021/acs.joc.0c02498] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
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The chemical synthesis of a highly hydrophobic membrane-associated peptide by native
chemical ligation (NCL) in an ionic liquid (IL) [C2mim][OAc]/buffer mixture
was achieved by employing peptide concentrations up to 11 mM. NCL was studied at
different pH and water content and compared to several “gold-standard”
ligation protocols. The optimized reaction protocol for the NCL in IL required the
addition of 40% water and pH adjustment to 7.0–7.5, resulting in ligation yields
of up to 80–95% within 1 to 4 h. This new ligation protocol is generally
applicable and outperforms current “gold-standard” NCL methods.
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Affiliation(s)
- Andreas C Baumruck
- Clemens-Schöpf Institute of Organic Chemistry and Biochemistry, Darmstadt University of Technology, Alarich-Weiss Straße 4, Darmstadt 64287, Germany
| | - Jie Yang
- Department of Chemistry and Molecular Biology, Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Kemigården 4, Göteborg 412 96, Sweden
| | - Gerke-Fabian Thomas
- Clemens-Schöpf Institute of Organic Chemistry and Biochemistry, Darmstadt University of Technology, Alarich-Weiss Straße 4, Darmstadt 64287, Germany
| | - Luisa I Beyer
- Department of Chemistry and Molecular Biology, Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Kemigården 4, Göteborg 412 96, Sweden
| | - Daniel Tietze
- Department of Chemistry and Molecular Biology, Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Kemigården 4, Göteborg 412 96, Sweden
| | - Alesia A Tietze
- Department of Chemistry and Molecular Biology, Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Kemigården 4, Göteborg 412 96, Sweden.,Clemens-Schöpf Institute of Organic Chemistry and Biochemistry, Darmstadt University of Technology, Alarich-Weiss Straße 4, Darmstadt 64287, Germany
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3
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Chisholm TS, Kulkarni SS, Hossain KR, Cornelius F, Clarke RJ, Payne RJ. Peptide Ligation at High Dilution via Reductive Diselenide-Selenoester Ligation. J Am Chem Soc 2019; 142:1090-1100. [DOI: 10.1021/jacs.9b12558] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | - Sameer S. Kulkarni
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
| | | | - Flemming Cornelius
- Department of Biomedicine, University of Aarhus, DK-8000 Aarhus C, Denmark
| | - Ronald J. Clarke
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
- The University of Sydney Nano Institute, Sydney, NSW 2006, Australia
| | - Richard J. Payne
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
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4
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Hayashi G, Yanase M, Nakatsuka Y, Okamoto A. Simultaneous and Traceless Ligation of Peptide Fragments on DNA Scaffold. Biomacromolecules 2019; 20:1246-1253. [PMID: 30677290 DOI: 10.1021/acs.biomac.8b01655] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Peptide ligation is an indispensable step in the chemical synthesis of target peptides and proteins that are difficult to synthesize at once by a solid-phase synthesis. The ligation reaction is generally conducted with two peptide fragments at a high aqueous concentration to increase the reaction rate; however, this often causes unpredictable aggregation and precipitation of starting or resulting peptides due to their hydrophobicities. Here, we have developed a novel peptide ligation strategy harnessing the two intrinsic characteristics of oligodeoxynucleotides (ODNs), i.e., their hydrophilicity and hybridization ability, which allowed increases in the water solubility of peptides and the reaction kinetics due to the proximity effect, respectively. Peptide-ODN conjugates that can be cleaved to regenerate native peptide sequences were synthesized using novel lysine derivatives containing conjugation handles and photolabile linkers, via solid-phase peptide synthesis and subsequent conjugation to 15-mer ODNs. Two complementary conjugates were applied to carbodiimide-mediated peptide ligation on a DNA scaffold, and the subsequent DNA removal was conducted by photoirradiation in a traceless fashion. This DNA scaffold-assisted ligation resulted in a significant acceleration of the reaction kinetics and enabled ligation of a hydrophobic peptide at a micromolar concentration. On the basis of this chemistry, a simultaneous ligation of three different peptide fragments on two different DNA scaffolds has been conducted for the first time.
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Affiliation(s)
- Gosuke Hayashi
- Department of Chemistry and Biotechnology , The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku , Tokyo 113-8656 , Japan
| | - Masafumi Yanase
- Department of Chemistry and Biotechnology , The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku , Tokyo 113-8656 , Japan
| | - Yu Nakatsuka
- Department of Chemistry and Biotechnology , The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku , Tokyo 113-8656 , Japan
| | - Akimitsu Okamoto
- Department of Chemistry and Biotechnology , The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku , Tokyo 113-8656 , Japan.,Research Center for Advanced Science and Technology , The University of Tokyo , 4-6-1 Komaba, Meguro-ku , Tokyo 153-8904 , Japan
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5
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Shapovalov G, Ritaine A, Bidaux G, Slomianny C, Borowiec AS, Gordienko D, Bultynck G, Skryma R, Prevarskaya N. Organelle membrane derived patches: reshaping classical methods for new targets. Sci Rep 2017; 7:14082. [PMID: 29074990 PMCID: PMC5658434 DOI: 10.1038/s41598-017-13968-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 10/04/2017] [Indexed: 12/12/2022] Open
Abstract
Intracellular ion channels are involved in multiple signaling processes, including such crucial ones as regulation of cellular motility and fate. With 95% of the cellular membrane belonging to intracellular organelles, it is hard to overestimate the importance of intracellular ion channels. Multiple studies have been performed on these channels over the years, however, a unified approach allowing not only to characterize their activity but also to study their regulation by partner proteins, analogous to the patch clamp “golden standard”, is lacking. Here, we present a universal approach that combines the extraction of intracellular membrane fractions with the preparation of patchable substrates that allows to characterize these channels in endogenous protein environment and to study their regulation by partner proteins. We validate this method by characterizing activity of multiple intracellular ion channels localized to different organelles and by providing detailed electrophysiological characterization of the regulation of IP3R activity by endogenous Bcl-2. Thus, after synthesis and reshaping of the well-established approaches, organelle membrane derived patch clamp provides the means to assess ion channels from arbitrary cellular membranes at the single channel level.
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Affiliation(s)
- George Shapovalov
- Inserm U1003, Equipe Labellisée par la Ligue Nationale Contre le Cancer, Université de Sciences et Technologies de Lille (USTL), F-59655, Villeneuve d'Ascq, France.,Laboratory of Excellence, Ion Channels Science and Therapeutics; Université Lille I Sciences et Technologies, Villeneuve d'Ascq, France
| | - Abigaël Ritaine
- Inserm U1003, Equipe Labellisée par la Ligue Nationale Contre le Cancer, Université de Sciences et Technologies de Lille (USTL), F-59655, Villeneuve d'Ascq, France.,Laboratory of Excellence, Ion Channels Science and Therapeutics; Université Lille I Sciences et Technologies, Villeneuve d'Ascq, France
| | - Gabriel Bidaux
- Inserm U1003, Equipe Labellisée par la Ligue Nationale Contre le Cancer, Université de Sciences et Technologies de Lille (USTL), F-59655, Villeneuve d'Ascq, France.,Laboratory of Excellence, Ion Channels Science and Therapeutics; Université Lille I Sciences et Technologies, Villeneuve d'Ascq, France.,Laboratoire INSERM U1060, CarMeN Laboratory, Claude Bernard Lyon 1 University, 8, avenue Rockfeller, F-69373, Lyon, France
| | - Christian Slomianny
- Inserm U1003, Equipe Labellisée par la Ligue Nationale Contre le Cancer, Université de Sciences et Technologies de Lille (USTL), F-59655, Villeneuve d'Ascq, France.,Laboratory of Excellence, Ion Channels Science and Therapeutics; Université Lille I Sciences et Technologies, Villeneuve d'Ascq, France
| | - Anne-Sophie Borowiec
- Inserm U1003, Equipe Labellisée par la Ligue Nationale Contre le Cancer, Université de Sciences et Technologies de Lille (USTL), F-59655, Villeneuve d'Ascq, France.,Laboratory of Excellence, Ion Channels Science and Therapeutics; Université Lille I Sciences et Technologies, Villeneuve d'Ascq, France.,Laboratoire INSERM U1060, CarMeN Laboratory, Claude Bernard Lyon 1 University, 8, avenue Rockfeller, F-69373, Lyon, France
| | - Dmitri Gordienko
- Inserm U1003, Equipe Labellisée par la Ligue Nationale Contre le Cancer, Université de Sciences et Technologies de Lille (USTL), F-59655, Villeneuve d'Ascq, France.,Laboratory of Excellence, Ion Channels Science and Therapeutics; Université Lille I Sciences et Technologies, Villeneuve d'Ascq, France
| | - Geert Bultynck
- KU Leuven, Laboratory of Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine, Herestraat 49, BE-3000, Leuven, Belgium
| | - Roman Skryma
- Inserm U1003, Equipe Labellisée par la Ligue Nationale Contre le Cancer, Université de Sciences et Technologies de Lille (USTL), F-59655, Villeneuve d'Ascq, France.,Laboratory of Excellence, Ion Channels Science and Therapeutics; Université Lille I Sciences et Technologies, Villeneuve d'Ascq, France
| | - Natalia Prevarskaya
- Inserm U1003, Equipe Labellisée par la Ligue Nationale Contre le Cancer, Université de Sciences et Technologies de Lille (USTL), F-59655, Villeneuve d'Ascq, France. .,Laboratory of Excellence, Ion Channels Science and Therapeutics; Université Lille I Sciences et Technologies, Villeneuve d'Ascq, France.
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6
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Howorka S. Building membrane nanopores. NATURE NANOTECHNOLOGY 2017; 12:619-630. [PMID: 28681859 DOI: 10.1038/nnano.2017.99] [Citation(s) in RCA: 188] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Accepted: 04/19/2017] [Indexed: 05/28/2023]
Abstract
Membrane nanopores-hollow nanoscale barrels that puncture biological or synthetic membranes-have become powerful tools in chemical- and biosensing, and have achieved notable success in portable DNA sequencing. The pores can be self-assembled from a variety of materials, including proteins, peptides, synthetic organic compounds and, more recently, DNA. But which building material is best for which application, and what is the relationship between pore structure and function? In this Review, I critically compare the characteristics of the different building materials, and explore the influence of the building material on pore structure, dynamics and function. I also discuss the future challenges of developing nanopore technology, and consider what the next-generation of nanopore structures could be and where further practical applications might emerge.
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Affiliation(s)
- Stefan Howorka
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, London WC1H 0AJ, UK
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7
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Li JB, Tang S, Zheng JS, Tian CL, Liu L. Removable Backbone Modification Method for the Chemical Synthesis of Membrane Proteins. Acc Chem Res 2017; 50:1143-1153. [PMID: 28374993 DOI: 10.1021/acs.accounts.7b00001] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Chemical synthesis can produce water-soluble globular proteins bearing specifically designed modifications. These synthetic molecules have been used to study the biological functions of proteins and to improve the pharmacological properties of protein drugs. However, the above advances notwithstanding, membrane proteins (MPs), which comprise 20-30% of all proteins in the proteomes of most eukaryotic cells, remain elusive with regard to chemical synthesis. This difficulty stems from the strong hydrophobic character of MPs, which can cause considerable handling issues during ligation, purification, and characterization steps. Considerable efforts have been made to improve the solubility of transmembrane peptides for chemical ligation. These methods can be classified into two main categories: the manipulation of external factors and chemical modification of the peptide. This Account summarizes our research advances in the development of chemical modification especially the two generations of removable backbone modification (RBM) strategy for the chemical synthesis of MPs. In the first RBM generation, we install a removable modification group at the backbone amide of Gly within the transmembrane peptides. In the second RBM generation, the RBM group can be installed into all primary amino acid residues. The second RBM strategy combines the activated intramolecular O-to-N acyl transfer reaction, in which a phenyl group remains unprotected during the coupling process, which can play a catalytic role to generate the activated phenyl ester to assist in the formation of amide. The key feature of the RBM group is its switchable stability in trifluoroacetic acid. The stability of these backbone amide N-modifications toward TFA can be modified by regulating the electronic effects of phenol groups. The free phenol group is acylated to survive the TFA deprotection step, while the acyl phenyl ester will be quantitatively hydrolyzed in a neutral aqueous solution, and the free phenol group increases the electron density of the benzene ring to make the RBM labile to TFA. The transmembrane peptide segment bearing RBM groups behaves like a water-soluble peptide during fluorenylmethyloxycarbonyl based solid-phase peptide synthesis (Fmoc SPPS), ligation, purification, and characterization. The quantitative removal of the RBM group can be performed to obtain full-length MPs. The RBM strategy was used to prepare the core transmembrane domain Kir5.1[64-179] not readily accessible by recombinant protein expression, the influenza A virus M2 proton channel with phosphorylation, the cation-specific ion channel p7 from the hepatitis C virus with site-specific NMR isotope labels, and so on. The RBM method enables the practical engineering of small- to medium-sized MPs or membrane protein domains to address fundamental questions in the biochemical, biophysical, and pharmaceutical sciences.
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Affiliation(s)
- Jia-Bin Li
- School of Life Sciences, University of Science and Technology of China , Hefei 230027, China
- Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University , Beijing 100084, China
| | - Shan Tang
- Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University , Beijing 100084, China
| | - Ji-Shen Zheng
- School of Life Sciences, University of Science and Technology of China , Hefei 230027, China
| | - Chang-Lin Tian
- School of Life Sciences, University of Science and Technology of China , Hefei 230027, China
| | - Lei Liu
- Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University , Beijing 100084, China
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8
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Li T, Liu H, Li X. Chemical Synthesis of HMGA1a Proteins with Post-translational Modifications via Ser/Thr Ligation. Org Lett 2016; 18:5944-5947. [DOI: 10.1021/acs.orglett.6b03056] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Tianlu Li
- Department of Chemistry,
State Key Lab of Synthetic Chemistry, The University of Hong Kong, Pokfulam, Hong Kong
| | - Heng Liu
- Department of Chemistry,
State Key Lab of Synthetic Chemistry, The University of Hong Kong, Pokfulam, Hong Kong
| | - Xuechen Li
- Department of Chemistry,
State Key Lab of Synthetic Chemistry, The University of Hong Kong, Pokfulam, Hong Kong
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9
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Maity SK, Mann G, Jbara M, Laps S, Kamnesky G, Brik A. Palladium-Assisted Removal of a Solubilizing Tag from a Cys Side Chain To Facilitate Peptide and Protein Synthesis. Org Lett 2016; 18:3026-9. [PMID: 27268382 DOI: 10.1021/acs.orglett.6b01442] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Reversible attachment of solubilizing tags to hydrophobic peptides to facilitate their purification and ligation is an essential yet challenging task in chemical protein synthesis. The efficient palladium-assisted removal of the solubilizing tag linked to the Cys side chain is reported. The strategy was applied for the efficient preparation of histone protein H4 from two fragments via one-pot operation of ligation, removal of the solubilizing tag, and desulfurization.
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Affiliation(s)
- Suman Kumar Maity
- Schulich Faculty of Chemistry Technion, Israel Institute of Technology , 32000 Haifa, Israel
| | - Guy Mann
- Schulich Faculty of Chemistry Technion, Israel Institute of Technology , 32000 Haifa, Israel
| | - Muhammad Jbara
- Schulich Faculty of Chemistry Technion, Israel Institute of Technology , 32000 Haifa, Israel
| | - Shay Laps
- Schulich Faculty of Chemistry Technion, Israel Institute of Technology , 32000 Haifa, Israel
| | - Guy Kamnesky
- Schulich Faculty of Chemistry Technion, Israel Institute of Technology , 32000 Haifa, Israel
| | - Ashraf Brik
- Schulich Faculty of Chemistry Technion, Israel Institute of Technology , 32000 Haifa, Israel
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10
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Zheng JS, He Y, Zuo C, Cai XY, Tang S, Wang ZA, Zhang LH, Tian CL, Liu L. Robust Chemical Synthesis of Membrane Proteins through a General Method of Removable Backbone Modification. J Am Chem Soc 2016; 138:3553-61. [PMID: 26943264 DOI: 10.1021/jacs.6b00515] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Chemical protein synthesis can provide access to proteins with post-translational modifications or site-specific labelings. Although this technology is finding increasing applications in the studies of water-soluble globular proteins, chemical synthesis of membrane proteins remains elusive. In this report, a general and robust removable backbone modification (RBM) method is developed for the chemical synthesis of membrane proteins. This method uses an activated O-to-N acyl transfer auxiliary to install in the Fmoc solid-phase peptide synthesis process a RBM group with switchable reactivity toward trifluoroacetic acid. The method can be applied to versatile membrane proteins because the RBM group can be placed at any primary amino acid. With RBM, the membrane proteins and their segments behave almost as if they were water-soluble peptides and can be easily handled in the process of ligation, purification, and mass characterizations. After the full-length protein is assembled, the RBM group can be readily removed by trifluoroacetic acid. The efficiency and usefulness of the new method has been demonstrated by the successful synthesis of a two-transmembrane-domain protein (HCV p7 ion channel) with site-specific isotopic labeling and a four-transmembrane-domain protein (multidrug resistance transporter EmrE). This method enables practical synthesis of small- to medium-sized membrane proteins or membrane protein domains for biochemical and biophysical studies.
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Affiliation(s)
- Ji-Shen Zheng
- High Magnetic Field Laboratory, Chinese Academy of Sciences, and School of Life Sciences, University of Science and Technology of China , Hefei 230031, China
| | - Yao He
- High Magnetic Field Laboratory, Chinese Academy of Sciences, and School of Life Sciences, University of Science and Technology of China , Hefei 230031, China
| | - Chao Zuo
- Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University , Beijing 100084, China
| | - Xiao-Ying Cai
- High Magnetic Field Laboratory, Chinese Academy of Sciences, and School of Life Sciences, University of Science and Technology of China , Hefei 230031, China
| | - Shan Tang
- Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University , Beijing 100084, China
| | - Zhipeng A Wang
- Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University , Beijing 100084, China
| | - Long-Hua Zhang
- High Magnetic Field Laboratory, Chinese Academy of Sciences, and School of Life Sciences, University of Science and Technology of China , Hefei 230031, China
| | - Chang-Lin Tian
- High Magnetic Field Laboratory, Chinese Academy of Sciences, and School of Life Sciences, University of Science and Technology of China , Hefei 230031, China
| | - Lei Liu
- Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University , Beijing 100084, China
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11
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Kwon B, Tietze D, White PB, Liao SY, Hong M. Chemical ligation of the influenza M2 protein for solid-state NMR characterization of the cytoplasmic domain. Protein Sci 2015; 24:1087-99. [PMID: 25966817 PMCID: PMC4500309 DOI: 10.1002/pro.2690] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Revised: 04/13/2015] [Accepted: 04/24/2015] [Indexed: 12/17/2022]
Abstract
Solid-state NMR-based structure determination of membrane proteins and large protein complexes faces the challenge of limited spectral resolution when the proteins are uniformly (13)C-labeled. A strategy to meet this challenge is chemical ligation combined with site-specific or segmental labeling. While chemical ligation has been adopted in NMR studies of water-soluble proteins, it has not been demonstrated for membrane proteins. Here we show chemical ligation of the influenza M2 protein, which contains a transmembrane (TM) domain and two extra-membrane domains. The cytoplasmic domain, which contains an amphipathic helix (AH) and a cytoplasmic tail, is important for regulating virus assembly, virus budding, and the proton channel activity. A recent study of uniformly (13)C-labeled full-length M2 by spectral simulation suggested that the cytoplasmic tail is unstructured. To further test this hypothesis, we conducted native chemical ligation of the TM segment and part of the cytoplasmic domain. Solid-phase peptide synthesis of the two segments allowed several residues to be labeled in each segment. The post-AH cytoplasmic residues exhibit random-coil chemical shifts, low bond order parameters, and a surface-bound location, thus indicating that this domain is a dynamic random coil on the membrane surface. Interestingly, the protein spectra are similar between a model membrane and a virus-mimetic membrane, indicating that the structure and dynamics of the post-AH segment is insensitive to the lipid composition. This chemical ligation approach is generally applicable to medium-sized membrane proteins to provide site-specific structural constraints, which complement the information obtained from uniformly (13)C, (15)N-labeled proteins.
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Affiliation(s)
- Byungsu Kwon
- Department of Chemistry, Massachusetts Institute of TechnologyCambridge, Massachusetts, 02139
| | - Daniel Tietze
- Department of Chemistry, Massachusetts Institute of TechnologyCambridge, Massachusetts, 02139
| | - Paul B White
- Department of Chemistry, Massachusetts Institute of TechnologyCambridge, Massachusetts, 02139
| | - Shu Y Liao
- Department of Chemistry, Massachusetts Institute of TechnologyCambridge, Massachusetts, 02139
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of TechnologyCambridge, Massachusetts, 02139
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12
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Abstract
The mechanosensitive channel of large conductance, MscL, has been proposed as a triggered nanovalve to be used in drug release and other nanodevices. It is a small homopentameric bacterial protein that has the largest gated pore known: greater than 30 Å. Large molecules, even small proteins can be released through MscL. Although MscL normally gates in response to membrane tension, early studies found that hydrophilic or charged residue substitutions near the constriction of the channel leads to pore opening. Researchers have successfully changed the modality of MscL to open to stimuli such as light by chemically modifying a single residue, G22, within the MscL pore. Here, by utilizing in vivo, liposome efflux, and patch clamp assays we compared modification of G22 with that of another neighboring residue, G26, and demonstrate that modifying G26 may be a better choice for triggered nanovalves used for triggered vesicular release of compounds.
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13
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Zuo C, Tang S, Zheng JS. Chemical synthesis and biophysical applications of membrane proteins. J Pept Sci 2014; 21:540-9. [DOI: 10.1002/psc.2721] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 10/30/2014] [Accepted: 10/31/2014] [Indexed: 12/16/2022]
Affiliation(s)
- Chao Zuo
- High Magnetic Field Laboratory; Chinese Academy of Sciences; Hefei 230031 China
- Department of Chemistry; Tsinghua University; Beijing 100084 China
| | - Shan Tang
- Department of Chemistry; Tsinghua University; Beijing 100084 China
| | - Ji-Shen Zheng
- High Magnetic Field Laboratory; Chinese Academy of Sciences; Hefei 230031 China
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14
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Thapa P, Zhang RY, Menon V, Bingham JP. Native chemical ligation: a boon to peptide chemistry. Molecules 2014; 19:14461-83. [PMID: 25221869 PMCID: PMC6271921 DOI: 10.3390/molecules190914461] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 09/02/2014] [Accepted: 09/02/2014] [Indexed: 11/16/2022] Open
Abstract
The use of chemical ligation within the realm of peptide chemistry has opened various opportunities to expand the applications of peptides/proteins in biological sciences. Expansion and refinement of ligation chemistry has made it possible for the entry of peptides into the world of viable oral therapeutic drugs through peptide backbone cyclization. This progression has been a journey of chemical exploration and transition, leading to the dominance of native chemical ligation in the present advances of peptide/protein applications. Here we illustrate and explore the historical and current nature of peptide ligation, providing a clear indication to the possibilities and use of these novel methods to take peptides outside their typically defined boundaries.
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Affiliation(s)
- Parashar Thapa
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Rui-Yang Zhang
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Vinay Menon
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Jon-Paul Bingham
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA.
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15
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Zheng JS, Yu M, Qi YK, Tang S, Shen F, Wang ZP, Xiao L, Zhang L, Tian CL, Liu L. Expedient total synthesis of small to medium-sized membrane proteins via Fmoc chemistry. J Am Chem Soc 2014; 136:3695-704. [PMID: 24559202 DOI: 10.1021/ja500222u] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Total chemical synthesis provides a unique approach for the access to uncontaminated, monodisperse, and more importantly, post-translationally modified membrane proteins. In the present study we report a practical procedure for expedient and cost-effective synthesis of small to medium-sized membrane proteins in multimilligram scale through the use of automated Fmoc chemistry. The key finding of our study is that after the attachment of a removable arginine-tagged backbone modification group, the membrane protein segments behave almost the same as ordinary water-soluble peptides in terms of Fmoc solid-phase synthesis, ligation, purification, and mass spectrometry characterization. The efficiency and practicality of the new method is demonstrated by the successful preparation of Ser64-phosphorylated M2 proton channel from influenza A virus and the membrane-embedded domain of an inward rectifier K(+) channel protein Kir5.1. Functional characterizations of these chemically synthesized membrane proteins indicate that they provide useful and otherwise-difficult-to-access materials for biochemistry and biophysics studies.
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Affiliation(s)
- Ji-Shen Zheng
- Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University , Beijing 100084, China
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16
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Dittmann M, Seidel R, Chizhov I, Engelhard M. Total chemical synthesis of a membrane protein domain analogue containing two transmembrane helices: functional reconstitution of the semisynthetic sensory rhodopsin/transducer complex. J Pept Sci 2014; 20:137-44. [DOI: 10.1002/psc.2605] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 11/25/2013] [Accepted: 11/25/2013] [Indexed: 12/15/2022]
Affiliation(s)
- Marc Dittmann
- Max Planck Institute of Molecular Physiology; Otto Hahn Str. 11 44227 Dortmund Germany
| | - Ralf Seidel
- Max Planck Institute of Molecular Physiology; Otto Hahn Str. 11 44227 Dortmund Germany
| | - Igor Chizhov
- Medizinische Hochschule Hannover; Carl-Neuberg-Str. 1 30625 Hannover Germany
| | - Martin Engelhard
- Max Planck Institute of Molecular Physiology; Otto Hahn Str. 11 44227 Dortmund Germany
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17
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Abstract
Potassium channels conduct K(+) ions selectively and at very high rates. Central to the function of K(+) channels is a structural unit called the selectivity filter. In the selectivity filter, a row of four K(+) binding sites are created using mainly the backbone carbonyl oxygen atoms. Due to the involvement of the protein backbone, site-directed mutagenesis is of limited utility in investigating the selectivity filter. In order to overcome this limitation, we have developed a semisynthetic approach, which permits the use of chemical synthesis to manipulate the selectivity filter. In this chapter, we describe the protocols that we have developed for the semisynthesis of the K(+) channel, KcsA. We anticipate that the protocols described in this chapter will also be applicable for the semisynthesis of other integral membrane proteins of interest.
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18
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Huang YC, Li YM, Chen Y, Pan M, Li YT, Yu L, Guo QX, Liu L. Synthesis of Autophagosomal Marker Protein LC3-II under Detergent-Free Conditions. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201209523] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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19
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Huang YC, Li YM, Chen Y, Pan M, Li YT, Yu L, Guo QX, Liu L. Synthesis of Autophagosomal Marker Protein LC3-II under Detergent-Free Conditions. Angew Chem Int Ed Engl 2013; 52:4858-62. [DOI: 10.1002/anie.201209523] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Revised: 02/06/2013] [Indexed: 11/10/2022]
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Doerner JF, Febvay S, Clapham DE. Controlled delivery of bioactive molecules into live cells using the bacterial mechanosensitive channel MscL. Nat Commun 2012; 3:990. [PMID: 22871809 PMCID: PMC3651673 DOI: 10.1038/ncomms1999] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Accepted: 07/10/2012] [Indexed: 12/22/2022] Open
Abstract
Bacterial mechanosensitive channels are some of the largest pores in nature. In particular, MscL, with a pore diameter >25 Å, allows passage of large organic ions and small proteins. Functional MscL reconstitution into lipids has been proposed for applications in vesicular-based drug release. Here we show that these channels can be functionally expressed in mammalian cells to afford rapid controlled uptake of membrane-impermeable molecules. We first demonstrate that MscL gating in response to increased membrane tension is preserved in mammalian cell membranes. Molecular delivery is controlled by adopting an established method of MscL charge-induced activation. We then determine pore size limitations using fluorescently labelled model cargoes. Finally, we activate MscL to introduce the cell-impermeable bi-cyclic peptide phalloidin, a specific marker for actin filaments, into cells. We propose that MscL will be a useful tool for gated and controlled delivery of bioactive molecules into cells.
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Affiliation(s)
- Julia F Doerner
- HHMI, Department of Cardiology, Boston Children's Hospital, Boston, Massachusetts 02115, USA
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21
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Balleza D. Mechanical properties of lipid bilayers and regulation of mechanosensitive function: from biological to biomimetic channels. Channels (Austin) 2012; 6:220-33. [PMID: 22790280 DOI: 10.4161/chan.21085] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Material properties of lipid bilayers, including thickness, intrinsic curvature and compressibility regulate the function of mechanosensitive (MS) channels. This regulation is dependent on phospholipid composition, lateral packing and organization within the membrane. Therefore, a more complete framework to understand the functioning of MS channels requires insights into bilayer structure, thermodynamics and phospholipid structure, as well as lipid-protein interactions. Phospholipids and MS channels interact with each other mainly through electrostatic forces and hydrophobic matching, which are also crucial for antimicrobial peptides. They are excellent models for studying the formation and stabilization of membrane pores. Importantly, they perform equivalent responses as MS channels: (1) tilting in response to tension and (2) dissipation of osmotic gradients. Lessons learned from pore forming peptides could enrich our knowledge of mechanisms of action and evolution of these channels. Here, the current state of the art is presented and general principles of membrane regulation of mechanosensitive function are discussed.
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Affiliation(s)
- Daniel Balleza
- Unidad de Biofísica, CSIC, UPV/EHU, Universidad del País Vasco, Leioa, Spain.
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22
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Dittmann M, Sadek M, Seidel R, Engelhard M. Native chemical ligation in dimethylformamide can be performed chemoselectively without racemization. J Pept Sci 2012; 18:312-6. [PMID: 22431434 DOI: 10.1002/psc.2401] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Revised: 01/04/2012] [Accepted: 01/10/2012] [Indexed: 11/11/2022]
Abstract
Native chemical ligation of unprotected peptides in organic solvents has been previously reported as a fast, efficient, and suitable method for coupling of hydrophobic peptides. However, it has not been determined whether the reaction can be carried out without possible side reactions or racemization. Here, we present a study on the chemoselectivity of this method by model reactions designed to test the reactivity of Arg and Lys side chains as well as that of α-amino groups. A possible racemization of the C-terminal amino acid of the N-terminal peptide was also investigated. The results show that ligation in organic solvents can be conducted chemoselectively without side reactions with other nucleophilic groups. Furthermore, no racemization of the C-terminal amino acid was observed if both educts were added simultaneously. Thus, native chemical ligation can be performed either in aqueous buffer systems or in organic solvents paving the way for the synthesis of larger hydrophobic peptides and/or membrane proteins.
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Affiliation(s)
- Marc Dittmann
- Max Planck Institute of Molecular Physiology, Otto Hahn Str. 11, 44227, Dortmund, Germany
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23
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Yang LM, Wray R, Parker J, Wilson D, Duran RS, Blount P. Three routes to modulate the pore size of the MscL channel/nanovalve. ACS NANO 2012; 6:1134-1141. [PMID: 22206349 PMCID: PMC3289768 DOI: 10.1021/nn203703j] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
MscL is a bacterial mechanosensitive channel that protects cells from lysis upon acute decrease in external osmotic environment. It is one of the best characterized mechanosensors known, thus serving as a paradigm of how such molecules sense and respond to stimuli. In addition, the fact that it can be genetically modified, expressed, isolated, and manipulated has led to its proposed use as a triggered nanovalve for various functions including sensors within microelectronic array chips, as well as vesicular-based targeted drug release. X-ray crystallography reveals a homopentameric complex with each subunit containing two transmembrane α-helices (TM1 and TM2) and a single carboxyl terminal α-helix arranging within the complex to form a 5-fold cytoplasmic bundle (CB), whose function and stability remain unclear. In this study, we show three routes that throttle the open channel conductance. When the linker between the TM2 and CB domain is shortened by deletions or constrained by either cross-linking or heavy metal coordination, the conductance of the channel is reduced; in the later two cases, even reversibly. While they have implications for the stability of the CB, these data also provide routes for engineering MscL sensors that are more versatile for potential nanotech devices.
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Affiliation(s)
- Li-Min Yang
- Department of Physiology, University of Texas Medical Center at Dallas, Dallas, Texas, USA
| | - Robin Wray
- Department of Physiology, University of Texas Medical Center at Dallas, Dallas, Texas, USA
| | - Juandell Parker
- Department of Physiology, University of Texas Medical Center at Dallas, Dallas, Texas, USA
| | - Danyell Wilson
- Department of Chemistry, University of Florida, current address Moffitt Cancer Center, Tampa, FL
| | - Randolph S. Duran
- Department of Chemistry, Louisiana State University, Baton Rouge, LA
| | - Paul Blount
- Department of Physiology, University of Texas Medical Center at Dallas, Dallas, Texas, USA
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24
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Mechanosensitive channels: what can they do and how do they do it? Structure 2012; 19:1356-69. [PMID: 22000509 DOI: 10.1016/j.str.2011.09.005] [Citation(s) in RCA: 240] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2011] [Revised: 09/19/2011] [Accepted: 09/20/2011] [Indexed: 12/16/2022]
Abstract
While mechanobiological processes employ diverse mechanisms, at their heart are force-induced perturbations in the structure and dynamics of molecules capable of triggering subsequent events. Among the best characterized force-sensing systems are bacterial mechanosensitive channels. These channels reflect an intimate coupling of protein conformation with the mechanics of the surrounding membrane; the membrane serves as an adaptable sensor that responds to an input of applied force and converts it into an output signal, interpreted for the cell by mechanosensitive channels. The cell can exploit this information in a number of ways: ensuring cellular viability in the presence of osmotic stress and perhaps also serving as a signal transducer for membrane tension or other functions. This review focuses on the bacterial mechanosensitive channels of large (MscL) and small (MscS) conductance and their eukaryotic homologs, with an emphasis on the outstanding issues surrounding the function and mechanism of this fascinating class of molecules.
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25
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Monbaliu JCM, Katritzky AR. Recent trends in Cys- and Ser/Thr-based synthetic strategies for the elaboration of peptide constructs. Chem Commun (Camb) 2012; 48:11601-22. [DOI: 10.1039/c2cc34434c] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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26
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Devaraneni PK, Devereaux JJ, Valiyaveetil FI. In vitro folding of KvAP, a voltage-gated K+ channel. Biochemistry 2011; 50:10442-50. [PMID: 22044112 DOI: 10.1021/bi2012965] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this contribution, we report in vitro folding of the archaebacterial voltage-gated K(+) channel, K(v)AP. We show that in vitro folding of the K(v)AP channel from the extensively unfolded state requires lipid vesicles and that the refolded channel is biochemically and functionally similar to the native channel. The in vitro folding process is slow at room temperature, and the folding yield depends on the composition of the lipid bilayer. The major factor influencing refolding is temperature, and almost quantitative refolding of the K(v)AP channel is observed at 80 °C. To differentiate between insertion into the bilayer and folding within the bilayer, we developed a cysteine protection assay. Using this assay, we demonstrate that insertion of the unfolded protein into the bilayer is relatively fast at room temperature and independent of lipid composition, suggesting that temperature and bilayer composition influence folding within the bilayer. Further, we demonstrate that in vitro folding provides an effective method for obtaining high yields of the native channel. Our studies suggest that the K(v)AP channel provides a good model system for investigating the folding of a multidomain integral membrane protein.
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Affiliation(s)
- Prasanna K Devaraneni
- The Program in Chemical Biology, Department of Physiology and Pharmacology, Oregon Health and Science University, Portland, Oregon 97239, United States
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27
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Shen F, Huang YC, Tang S, Chen YX, Liu L. Chemical Synthesis of Integral Membrane Proteins: Methods and Applications. Isr J Chem 2011. [DOI: 10.1002/ijch.201100076] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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28
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Brehs M, Bäuml K, Becker CFW. Chemical Synthesis of an Integral Membrane Enzyme - The Challenges of Diacylglycerol Kinase. Isr J Chem 2011. [DOI: 10.1002/ijch.201100090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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29
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Balleza D. Toward understanding protocell mechanosensation. ORIGINS LIFE EVOL B 2011; 41:281-304. [PMID: 21080073 DOI: 10.1007/s11084-010-9225-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2010] [Accepted: 10/20/2010] [Indexed: 01/11/2023]
Abstract
Mechanosensitive (MS) channels can prevent bacterial bursting during hypo-osmotic shocks by responding to increases in lateral tension at the membrane level through an integrated and coordinated opening mechanism. Mechanical regulation in protocells could have been one of the first mechanisms to evolve in order to preserve their integrity against changing environmental conditions. How has the rich functional diversity found in present cells been created throughout evolution, and what did the primordial MS channels look like? This review has been written with the aim of identifying which factors may have been important for the appearance of the first osmotic valve in a prebiotic context, and what this valve may have been like. It highlights the mechanical properties of lipid bilayers, the association of peptides as aggregates in membranes, and the conservation of sequence motifs as central aspects to understand the evolution of proteins that gate below the tension required for spontaneous pore formation and membrane rupture. The arguments developed here apply to both MscL and MscS homologs, but could be valid to mechano-susceptible proteins in general.
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Affiliation(s)
- Daniel Balleza
- Unidad de Biofísica, CSIC-UPV/EHU, Universidad del País Vasco, Barrio Sarriena s/n, Leioa, Spain.
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30
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Lahiri S, Brehs M, Olschewski D, Becker CFW. Total Chemical Synthesis of an Integral Membrane Enzyme: Diacylglycerol Kinase fromEscherichia coli. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201006686] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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31
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Lahiri S, Brehs M, Olschewski D, Becker CFW. Total chemical synthesis of an integral membrane enzyme: diacylglycerol kinase from Escherichia coli. Angew Chem Int Ed Engl 2011; 50:3988-92. [PMID: 21433227 DOI: 10.1002/anie.201006686] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Revised: 02/14/2011] [Indexed: 12/17/2022]
Affiliation(s)
- Sunanda Lahiri
- Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
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32
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Dorwart MR, Wray R, Brautigam CA, Jiang Y, Blount P. S. aureus MscL is a pentamer in vivo but of variable stoichiometries in vitro: implications for detergent-solubilized membrane proteins. PLoS Biol 2010; 8:e1000555. [PMID: 21151884 PMCID: PMC2998437 DOI: 10.1371/journal.pbio.1000555] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Accepted: 10/27/2010] [Indexed: 12/03/2022] Open
Abstract
Detergent-induced rearrangements of membrane-protein subunits explain why two MscL channel stoichiometries have been resolved by X-ray crystallography - but S. aureus MscL is truly a pentamer in vivo. While the bacterial mechanosensitive channel of large conductance (MscL) is the best studied biological mechanosensor and serves as a paradigm for how a protein can sense and respond to membrane tension, the simple matter of its oligomeric state has led to debate, with models ranging from tetramers to hexamers. Indeed, two different oligomeric states of the bacterial mechanosensitive channel MscL have been resolved by X-ray crystallography: The M. tuberculosis channel (MtMscL) is a pentamer, while the S. aureus protein (SaMscL) forms a tetramer. Because several studies suggest that, like MtMscL, the E. coli MscL (EcoMscL) is a pentamer, we re-investigated the oligomeric state of SaMscL. To determine the structural organization of MscL in the cell membrane we developed a disulfide-trapping approach. Surprisingly, we found that virtually all SaMscL channels in vivo are pentameric, indicating this as the physiologically relevant and functional oligomeric state. Complementing our in vivo results, we purified SaMscL and assessed its oligomeric state using three independent approaches (sedimentation equilibrium centrifugation, crosslinking, and light scattering) and established that SaMscL is a pentamer when solubilized in Triton X-100 and C8E5 detergents. However, performing similar experiments on SaMscL solubilized in LDAO, the detergent used in the crystallographic study, confirmed the tetrameric oligomerization resolved by X-ray crystallography. We further demonstrate that this stoichiometric shift is reversible by conventional detergent exchange experiments. Our results firmly establish the pentameric organization of SaMscL in vivo. Furthermore they demonstrate that detergents can alter the subunit stoichiometry of membrane protein complexes in vitro; thus, in vivo assays are necessary to firmly establish a membrane protein's true functionally relevant oligomeric state. The ability to detect mechanical forces is at the basis of not only the senses of touch hearing and balance but also cardiovascular and osmotic regulation. One of the primary ways that organisms detect forces is through mechanosensitive channels, and mechanosensation is so vital that essentially all organisms have at least one such sensor. Indeed, the best-studied mechanosensitive channel is from bacteria, and because relatively little is known of mechanosensors from higher organisms, these channels are a model for how a protein can sense and respond to mechanical forces. Although the bacterial mechanosensitive channel MscL has been well studied, the simple issue of how many subunits it has is hotly debated. There are even two published crystal structures showing either tetrameric or pentameric complexes. Here we show that the channel is actually pentameric in vivo and that the detergent used to solubilize the protein can rearrange the complexes from pentamers to tetramers. The finding that detergents can have such a profound effect on structure may have broad implications for the study of other membrane proteins.
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Affiliation(s)
- Michael R. Dorwart
- Department of Physiology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America
| | - Robin Wray
- Department of Physiology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America
| | - Chad A. Brautigam
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America
| | - Youxing Jiang
- Department of Physiology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America
| | - Paul Blount
- Department of Physiology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America
- * E-mail:
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Focke PJ, Valiyaveetil FI. Studies of ion channels using expressed protein ligation. Curr Opin Chem Biol 2010; 14:797-802. [PMID: 20965773 DOI: 10.1016/j.cbpa.2010.09.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2010] [Accepted: 09/20/2010] [Indexed: 10/18/2022]
Abstract
Expressed protein ligation (EPL) is a semisynthetic technique for the chemoselective ligation of a synthetic peptide to a recombinant peptide that results in a native peptide bond at the ligation site. EPL therefore allows us to engineer proteins with chemically defined, site-specific modifications. While EPL has been used mainly in investigations of soluble proteins, in recent years it has been increasingly used in investigations of integral membrane proteins. These include studies on the KcsA K(+) channel, the non-selective cation channel NaK, and the porin OmpF. These studies are discussed in this review.
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Affiliation(s)
- Paul J Focke
- Program in Chemical Biology, Department of Physiology and Pharmacology, Oregon Health Sciences University, 3181 SW Sam Jackson Park Rd, Portland, OR 97239, USA
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Yang LM, Blount P. Manipulating the permeation of charged compounds through the MscL nanovalve. FASEB J 2010; 25:428-34. [PMID: 20930114 DOI: 10.1096/fj.10-170076] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
MscL is a bacterial mechanosensor that serves as a biological emergency release valve, releasing cytoplasmic solutes to the environment on osmotic downshock. Previous studies have recognized that this channel has properties that make it ideal for use as a triggered nanovalve for vesicular-based targeted drug-release devices. One can even change the modality of the sensor. Briefly, the introduction of charges into the MscL pore lumen gates the channel in the absence of membrane tension; thus, by inserting compounds that acquire a charge on exposure to an alternative stimulus, such as light or pH, into the pore of the channel, controllable nanoswitches that detect these alternative modalities have been engineered. However, a charge in the pore lumen could not only encourage actuation of the nanopore but also have a significant influence on the permeation of large charged compounds, which would thus have important implications for the efficiency of drug-release devices. In this study, we used in vivo and electrophysiological approaches to demonstrate that the introduction of a charge into pore lumen of MscL does indeed influence the permeation of charged molecules. These effects were more drastic for larger compounds and, surprisingly, were related to the orientation of the MscL channel in the membrane.
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Affiliation(s)
- Li-Min Yang
- Department of Physiology, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
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35
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Dittmann M, Sauermann J, Seidel R, Zimmermann W, Engelhard M. Native chemical ligation of hydrophobic peptides in organic solvents. J Pept Sci 2010; 16:558-62. [DOI: 10.1002/psc.1285] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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36
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Bayley H, Cheley S, Harrington L, Syeda R. Wrestling with native chemical ligation. ACS Chem Biol 2009; 4:983-5. [PMID: 20017575 DOI: 10.1021/cb900304p] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
An improved method for the semisynthesis of a potassium channel involving native chemical ligation allows the introduction of short sequences containing non-canonical amino acids at any position within the polypeptide chain. The work enhances the technology available for a range of fundamental investigations of membrane proteins and for applications of membrane channels and pores in biotechnology.
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Affiliation(s)
- Hagan Bayley
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Stephen Cheley
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Leon Harrington
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Ruhma Syeda
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
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37
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Komarov AG, Linn KM, Devereaux JJ, Valiyaveetil FI. Modular strategy for the semisynthesis of a K+ channel: investigating interactions of the pore helix. ACS Chem Biol 2009; 4:1029-38. [PMID: 19803500 DOI: 10.1021/cb900210r] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Chemical synthesis is a powerful method for precise modification of the structural and electronic properties of proteins. The difficulties in the synthesis and purification of peptides containing transmembrane segments have presented obstacles to the chemical synthesis of integral membrane proteins. Here, we present a modular strategy for the semisynthesis of integral membrane proteins in which solid-phase peptide synthesis is limited to the region of interest, while the rest of the protein is obtained by recombinant means. This modular strategy considerably simplifies the synthesis and purification steps that have previously hindered the chemical synthesis of integral membrane proteins. We develop a SUMO fusion and proteolysis approach for obtaining the N-terminal cysteine containing membrane-spanning peptides required for the semisynthesis. We demonstrate the feasibility of the modular approach by the semisynthesis of full-length KcsA K(+) channels in which only regions of interest, such as the selectivity filter or the pore helix, are obtained by chemical synthesis. The modular approach is used to investigate the hydrogen bond interactions of a tryptophan residue in the pore helix, tryptophan 68, by substituting it with the isosteric analogue, beta-(3-benzothienyl)-l-alanine (3BT). A functional analysis of the 3BT mutant channels indicates that the K(+) conduction and selectivity of the 3BT mutant channels are similar to those of the wild type, but the mutant channels show a 3-fold increase in Rb(+) conduction. These results suggest that the hydrogen bond interactions of tryptophan 68 are essential for optimizing the selectivity filter for K(+) conduction over Rb(+) conduction.
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Affiliation(s)
- Alexander G. Komarov
- Program in Chemical Biology, Department of Physiology and Pharmacology, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239
| | - Kellie M. Linn
- Program in Chemical Biology, Department of Physiology and Pharmacology, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239
| | - Jordan J. Devereaux
- Program in Chemical Biology, Department of Physiology and Pharmacology, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239
| | - Francis I. Valiyaveetil
- Program in Chemical Biology, Department of Physiology and Pharmacology, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239
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Coïc YM, Lan CL, Neumann JM, Jamin N, Baleux F. Slightly modifying pseudoproline dipeptides incorporation strategy enables solid phase synthesis of a 54 AA fragment of caveolin-1 encompassing the intramembrane domain. J Pept Sci 2009; 16:98-104. [DOI: 10.1002/psc.1203] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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39
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Abstract
The ability to selectively conduct K(+) ions is central to the function of K(+) channels. Selection for K(+) and rejection of Na(+) takes place in a conserved structural element referred to as the selectivity filter. The selectivity filter consists of four K(+)-specific ion binding sites that are created using predominantly the backbone carbonyl oxygen atoms. Due to the involvement of the protein backbone, experimental manipulation of the ion binding sites in the selectivity filter is not possible using traditional site directed mutagenesis. The limited suitability of the site-directed mutagenesis for studies on the selectivity filter has motivated the development of a semisynthesis approach, which enables the use of chemical synthesis to manipulate the selectivity filter. In this chapter, we describe the protocols that are presently used in our laboratory for the semisynthesis of the bacterial K(+) channel, KcsA. We show the introduction of a spectroscopic probe into the KcsA channel using semisynthesis. We also review previous applications of semisynthesis in investigations of K(+) channels. While the protocols described in this chapter are for the KcsA K(+) channel, we anticipate that similar protocols will also be applicable for the semisynthesis of other integral membrane proteins.
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Affiliation(s)
- Alexander G Komarov
- Program in Chemical Biology, Department of Physiology and Pharmacology, Oregon Health and Sciences University, Portland, Oregon, USA
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40
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41
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Olschewski D, Becker CFW. Chemical synthesis and semisynthesis of membrane proteins. MOLECULAR BIOSYSTEMS 2008; 4:733-40. [DOI: 10.1039/b803248c] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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42
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43
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Ingale S, Buskas T, Boons GJ. Synthesis of glyco(lipo)peptides by liposome-mediated native chemical ligation. Org Lett 2007; 8:5785-8. [PMID: 17134272 DOI: 10.1021/ol062423x] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Although native chemical ligation (NCL) is emerging as a powerful method for the assembly of (glyco)peptide building blocks, its applicability is reduced when peptide segments are poorly soluble in aqueous buffer. We have found that incorporating reactants in liposomes allows NCL of lipophilic peptides and lipopeptides. Furthermore, the reaction rates of liposome-mediated NCL are higher than traditional reaction conditions resulting in improved yields. [reaction: see text]
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Affiliation(s)
- Sampat Ingale
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
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44
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Rajagopal S, Kent SBH. Total chemical synthesis and biophysical characterization of the minimal isoform of the KChIP2 potassium channel regulatory subunit. Protein Sci 2007; 16:2056-64. [PMID: 17660260 PMCID: PMC2206977 DOI: 10.1110/ps.072876107] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The potassium channel accessory subunit KChIP2 associates with Kv4.2 channels in the cardiac myocyte and is involved in the regulation of the transient outward current (I(to)) during the early phase of repolarization of the action potential. As a first step to biophysically probe the mechanism of KChIP2, we have chemically synthesized its minimal isoform, KChIP2d, using Boc chemistry solid phase peptide synthesis in conjunction with native chemical ligation. The synthetic KChIP2d protein is primarily alpha-helical as predicted and becomes more structured upon binding calcium as assessed by (1)H-NMR and CD spectroscopy. Synthetic KChIP2d is in a monomer-dimer equilibrium in solution, and there is evidence for two monomer binding sites on an N-terminal peptide of Kv4.2. Planned future studies include the incorporation of fluorescent and spin labeled probes in KChIP2d to yield structural information in parallel with electrophysiologic studies to elucidate KChIP2d's mechanism of action.
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Affiliation(s)
- Sudarshan Rajagopal
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA.
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45
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Johnson EC, Kent SB. Towards the total chemical synthesis of integral membrane proteins: a general method for the synthesis of hydrophobic peptide-thioester building blocks. Tetrahedron Lett 2007; 48:1795-1799. [PMID: 19177172 PMCID: PMC2631171 DOI: 10.1016/j.tetlet.2007.01.030] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Modification of a peptide-(α)thioester with a sequence of six arginines on the thioester leaving group can render soluble all peptides derived from a polytopic integral membrane protein. This strategy greatly simplifies the synthesis of peptide-(α)thioester building blocks for the total chemical synthesis of integral membrane proteins by native chemical ligation.
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Affiliation(s)
- Erik C.B. Johnson
- Institute for Biophysical Dynamics, 929 E. 57 Street, Chicago, IL 60637, USA
- Department of Biochemistry, 929 E. 57 Street, Chicago, IL 60637, USA
| | - Stephen B.H. Kent
- Institute for Biophysical Dynamics, 929 E. 57 Street, Chicago, IL 60637, USA
- Department of Biochemistry, 929 E. 57 Street, Chicago, IL 60637, USA
- Department of Chemistry, 929 E. 57 Street, Chicago, IL 60637, USA
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46
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Shim JW, Yang M, Gu LQ. In vitro synthesis, tetramerization and single channel characterization of virus-encoded potassium channel Kcv. FEBS Lett 2007; 581:1027-34. [PMID: 17316630 DOI: 10.1016/j.febslet.2007.02.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2007] [Revised: 02/02/2007] [Accepted: 02/02/2007] [Indexed: 10/23/2022]
Abstract
Chlorella virus-encoded membrane protein Kcv represents a new class of potassium channel. This 94-amino acids miniature K(+) channel consists of two trans-membrane alpha-helix domains intermediated by a pore domain that contains a highly conserved K(+) selectivity filter. Therefore, as an archetypal K(+) channel, the study of Kcv may yield valuable insights into the structure-function relationships underlying this important class of ion channel. Here, we report a series of new properties of Kcv. We first verified Kcv can be synthesized in vitro. By co-synthesis and assembly of wild-type and the tagged version of Kcv, we were able to demonstrate a tetrameric stoichiometry, a molecular structure adopted by all known K(+) channels. Most notably, the tetrameric Kcv complex retains its functional integrity in SDS (strong detergent)-containing solutions, a useful feature that allows for direct purification of protein from polyacrylamide gel. Once purified, the tetramer can form single potassium-selective ion channels in a lipid bilayer with functions consistent to the heterologously expressed Kcv. These finding suggest that the synthetic Kcv can serve as a model of virus-encoded K(+) channels; and its newly identified properties can be applied to the future study on structure-determined mechanisms such as K(+) channel functional stoichiometry.
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Affiliation(s)
- Ji Wook Shim
- Department of Biological Engineering, Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO 65211, USA
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47
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MscL: The Bacterial Mechanosensitive Channel of Large Conductance. MECHANOSENSITIVE ION CHANNELS, PART A 2007. [DOI: 10.1016/s1063-5823(06)58008-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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48
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Ohta Y, Itoh S, Shigenaga A, Shintaku S, Fujii N, Otaka A. Cysteine-derived s-protected oxazolidinones: potential chemical devices for the preparation of peptide thioesters. Org Lett 2006; 8:467-70. [PMID: 16435861 DOI: 10.1021/ol052755m] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[reaction: see text]. An N-S acyl-transfer-mediated preparation of peptide thioesters using the S-protected oxazolidinone derived from cysteine has been developed and applied to the synthesis of a 32-mer biologically active peptide by native chemical ligation protocols.
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Affiliation(s)
- Yusuke Ohta
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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49
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Arkin IT. Isotope-edited IR spectroscopy for the study of membrane proteins. Curr Opin Chem Biol 2006; 10:394-401. [PMID: 16935550 PMCID: PMC7185810 DOI: 10.1016/j.cbpa.2006.08.013] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2006] [Accepted: 08/15/2006] [Indexed: 11/25/2022]
Abstract
Fourier transform infrared (FTIR) spectroscopy has long been a powerful tool for structural analysis of membrane proteins. However, because of difficulties in resolving contributions from individual residues, most of the derived measurements tend to yield average properties for the system under study. Isotope editing, through its ability to resolve individual vibrations, establishes FTIR as a method that is capable of yielding accurate structural data on individual sites in a protein.
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Affiliation(s)
- Isaiah T Arkin
- The Alexander Silberman Institute of Life Sciences, Department of Biological Chemistry, The Hebrew University of Jerusalem, Edmund J Safra Campus, Givat-Ram, Jerusalem, Israel.
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50
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Booth PJ, Curnow P. Membrane proteins shape up: understanding in vitro folding. Curr Opin Struct Biol 2006; 16:480-8. [PMID: 16815700 DOI: 10.1016/j.sbi.2006.06.004] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2006] [Revised: 05/19/2006] [Accepted: 06/20/2006] [Indexed: 11/23/2022]
Abstract
Progress in structural biology has begun to reveal the precise architecture of integral membrane proteins. However, the manner in which these complex structures are achieved remains unclear. Recent developments are starting to shed light on the unfolding and folding of a small but growing number of membrane proteins. Mechanistic details derived from kinetic and thermodynamic experiments now enable comparison of the folding of different membrane proteins and their water-soluble cousins. This work also has important implications for other structural and functional studies of membrane proteins in vitro.
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Affiliation(s)
- Paula J Booth
- Department of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK.
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