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Yamamoto T, Yasuda S, Kasai RS, Nakano R, Hikiri S, Sugaya K, Hayashi T, Ogasawara S, Shiroishi M, Fujiwara TK, Kinoshita M, Murata T. A methodology for creating mutants of G-protein coupled receptors stabilized in active state by combining statistical thermodynamics and evolutionary molecular engineering. Protein Sci 2022; 31:e4425. [PMID: 36173170 PMCID: PMC9490800 DOI: 10.1002/pro.4425] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 08/09/2022] [Accepted: 08/12/2022] [Indexed: 09/28/2023]
Abstract
We challenged the stabilization of a G-protein coupled receptor (GPCR) in the active state solely by multiple amino-acid mutations without the agonist binding. For many GPCRs, the free energy of the active state is higher than that of the inactive state. When the inactive state is stabilized through the lowering of its free energy, the apparent midpoint temperature of thermal denaturation Tm exhibits a significant increase. However, this is not always the case for the stabilization of the active state. We constructed a modified version of our methodology combining statistical thermodynamics and evolutionary molecular engineering, which was recently developed for the inactive state. First, several residues to be mutated are determined using our statistical-thermodynamics theory. Second, a gene (mutant) library is constructed using Escherichia coli cells to efficiently explore most of the mutational space. Third, for the mutant screening, the mutants prepared in accordance with the library are expressed in engineered Saccharomyces cerevisiae YB14 cells which can grow only when a GPCR mutant stabilized in the active state has signaling function. For the adenosine A2A receptor tested, the methodology enabled us to sort out two triple mutants and a double mutant. It was experimentally corroborated that all the mutants exhibit much higher binding affinity for G protein than the wild type. Analyses indicated that the mutations make the structural characteristics shift toward those of the active state. However, only slight increases in Tm resulted from the mutations, suggesting the unsuitability of Tm to the stability measure for the active state.
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Affiliation(s)
- Taisei Yamamoto
- Department of Chemistry, Graduate School of ScienceChiba UniversityChibaJapan
| | - Satoshi Yasuda
- Department of Chemistry, Graduate School of ScienceChiba UniversityChibaJapan
- Membrane Protein Research CenterChiba UniversityChibaJapan
- Molecular Chirality Research CenterChiba UniversityChibaJapan
| | - Rinshi S. Kasai
- Institute for Glyco‐core Research (iGCORE)Gifu UniversityGifuJapan
- Institute for Life and Medical SciencesKyoto UniversityKyotoJapan
| | - Ryosuke Nakano
- Department of Chemistry, Graduate School of ScienceChiba UniversityChibaJapan
| | - Simon Hikiri
- Graduate School of Engineering ScienceOsaka UniversityOsakaJapan
| | - Kanna Sugaya
- Department of Chemistry, Graduate School of ScienceChiba UniversityChibaJapan
| | - Tomohiko Hayashi
- Interdisciplinary Program of Biomedical Engineering, Assistive Technology, and Art and Sports Sciences, Faculty of EngineeringNiigata UniversityNiigataJapan
- Institute of Advanced EnergyKyoto UniversityKyotoJapan
| | - Satoshi Ogasawara
- Department of Chemistry, Graduate School of ScienceChiba UniversityChibaJapan
- Membrane Protein Research CenterChiba UniversityChibaJapan
- Molecular Chirality Research CenterChiba UniversityChibaJapan
- Institute for Advanced Academic ResearchChiba UniversityChibaJapan
| | - Mitsunori Shiroishi
- Department of Biological Science and TechnologyTokyo University of ScienceTokyoJapan
| | - Takahiro K. Fujiwara
- Institute for Integrated Cell‐Material Sciences (WPI‐iCeMS)Kyoto UniversityKyotoJapan
| | - Masahiro Kinoshita
- Department of Chemistry, Graduate School of ScienceChiba UniversityChibaJapan
- Membrane Protein Research CenterChiba UniversityChibaJapan
- Institute of Advanced EnergyKyoto UniversityKyotoJapan
- Center for the Promotion of Interdisciplinary Education and ResearchKyoto UniversityKyoto‐shiJapan
| | - Takeshi Murata
- Department of Chemistry, Graduate School of ScienceChiba UniversityChibaJapan
- Membrane Protein Research CenterChiba UniversityChibaJapan
- Molecular Chirality Research CenterChiba UniversityChibaJapan
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Jain AR, Britton ZT, Markwalter CE, Robinson AS. Improved ligand-binding- and signaling-competent human NK2R yields in yeast using a chimera with the rat NK2R C-terminus enable NK2R-G protein signaling platform. Protein Eng Des Sel 2020; 32:459-469. [PMID: 32400863 DOI: 10.1093/protein/gzaa009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 03/09/2020] [Accepted: 04/16/2020] [Indexed: 02/07/2023] Open
Abstract
The tachykinin 2 receptor (NK2R) plays critical roles in gastrointestinal, respiratory and mental disorders and is a well-recognized target for therapeutic intervention. To date, therapeutics targeting NK2R have failed to meet regulatory agency approval due in large part to the limited characterization of the receptor-ligand interaction and downstream signaling. Herein, we report a protein engineering strategy to improve ligand-binding- and signaling-competent human NK2R that enables a yeast-based NK2R signaling platform by creating chimeras utilizing sequences from rat NK2R. We demonstrate that NK2R chimeras incorporating the rat NK2R C-terminus exhibited improved ligand-binding yields and downstream signaling in engineered yeast strains and mammalian cells, where observed yields were better than 4-fold over wild type. This work builds on our previous studies that suggest exchanging the C-termini of related and well-expressed family members may be a general protein engineering strategy to overcome limitations to ligand-binding and signaling-competent G protein-coupled receptor yields in yeast. We expect these efforts to result in NK2R drug candidates with better characterized signaling properties.
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Affiliation(s)
- Abhinav R Jain
- Department of Chemical and Biomolecular Engineering, Tulane University, 6823 St Charles Ave, New Orleans, LA, 70118, USA
| | - Zachary T Britton
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy St, Newark, DE, 19716, USA.,AstraZeneca, Antibody Discovery and Protein Engineering, Gaithersburg, MD 20878, USA
| | - Chester E Markwalter
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy St, Newark, DE, 19716, USA.,Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Anne S Robinson
- Department of Chemical and Biomolecular Engineering, Tulane University, 6823 St Charles Ave, New Orleans, LA, 70118, USA.,Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy St, Newark, DE, 19716, USA.,Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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Jain AR, Robinson AS. Functional Expression of Adenosine A 3 Receptor in Yeast Utilizing a Chimera with the A 2AR C-Terminus. Int J Mol Sci 2020; 21:E4547. [PMID: 32604732 PMCID: PMC7352405 DOI: 10.3390/ijms21124547] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 06/21/2020] [Accepted: 06/24/2020] [Indexed: 11/26/2022] Open
Abstract
The adenosine A3 receptor (A3R) is the only adenosine receptor subtype to be overexpressed in inflammatory and cancer cells and therefore is considered a novel and promising therapeutic target for inflammatory diseases and cancer. Heterologous expression of A3R at levels to allow biophysical characterization is a major bottleneck in structure-guided drug discovery efforts. Here, we apply protein engineering using chimeric receptors to improve expression and activity in yeast. Previously we had reported improved expression and trafficking of the chimeric A1R variant using a similar approach. In this report, we constructed chimeric A3/A2AR comprising the N-terminus and transmembrane domains from A3R (residues 1-284) and the cytoplasmic C-terminus of the A2AR (residues 291-412). The chimeric receptor showed approximately 2-fold improved expression with a 2-fold decreased unfolded protein response when compared to wild type A3R. Moreover, by varying culture conditions such as initial cell density and induction temperature a further 1.7-fold increase in total receptor yields was obtained. We observed native-like coupling of the chimeric receptor to Gai-Gpa1 in engineered yeast strains, activating the downstream, modified MAPK pathway. This strategy of utilizing chimeric receptor variants in yeast thus provides an exciting opportunity to improve expression and activity of "difficult-to-express" receptors, expanding the opportunity for utilizing yeast in drug discovery.
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Affiliation(s)
- Abhinav R. Jain
- Department of Chemical and Biomolecular Engineering, Tulane University, 6823 St Charles Ave, New Orleans, LA 70118, USA;
| | - Anne S. Robinson
- Department of Chemical and Biomolecular Engineering, Tulane University, 6823 St Charles Ave, New Orleans, LA 70118, USA;
- Department of Chemical Engineering, Carnegie Mellon University, 5000 Forbes Ave, Pittsburgh, PA 15213, USA
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4
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González M, Brito N, Hernández‐Bolaños E, González C. New tools for high-throughput expression of fungal secretory proteins in Saccharomyces cerevisiae and Pichia pastoris. Microb Biotechnol 2019; 12:1139-1153. [PMID: 30289201 PMCID: PMC6801181 DOI: 10.1111/1751-7915.13322] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 09/11/2018] [Accepted: 09/12/2018] [Indexed: 01/08/2023] Open
Abstract
Heterologous protein expression in yeast, mostly in Saccharomyces cerevisiae and Pichia pastoris, is a well-established and widely used technique. It typically requires the construction of an expression vector in Escherichia coli containing the foreign gene and its subsequent transformation into yeast. Although simple, this procedure has important limitations for the expression of large numbers of proteins, that is, for the generation of protein libraries. We describe here the development of a novel system for the easy and fast expression of heterologous proteins both in S. cerevisiae and in P. pastoris, under the control of the GAL1 and AOX1 promoters respectively. Expression in S. cerevisiae requires only the transformation of yeast cells with an unpurified PCR product carrying the gene to be expressed, and the expression of the same gene in P. pastoris requires only the isolation of the plasmid generated in S. cerevisiae and its transformation into this second yeast, thus making this system suitable for high-throughput projects. The system has been tested by the extracellular expression of 30 secretory fungal proteins.
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Affiliation(s)
- Mario González
- Departamento de BioquímicaMicrobiología, Biología Celular y GenéticaUniversidad de La Laguna38206La Laguna (Tenerife)Spain
| | - Nélida Brito
- Departamento de BioquímicaMicrobiología, Biología Celular y GenéticaUniversidad de La Laguna38206La Laguna (Tenerife)Spain
| | - Eduardo Hernández‐Bolaños
- Departamento de BioquímicaMicrobiología, Biología Celular y GenéticaUniversidad de La Laguna38206La Laguna (Tenerife)Spain
| | - Celedonio González
- Departamento de BioquímicaMicrobiología, Biología Celular y GenéticaUniversidad de La Laguna38206La Laguna (Tenerife)Spain
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Jain AR, Stradley SH, Robinson AS. The A2aR C-terminus provides improved total and active expression yields for adenosine receptor chimeras. AIChE J 2018. [DOI: 10.1002/aic.16398] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Abhinav R. Jain
- Dept. of Chemical and Biomolecular Engineering; Tulane University; New Orleans LA 70118
| | - Steven H. Stradley
- Dept. of Chemical and Biomolecular Engineering; Tulane University; New Orleans LA 70118
| | - Anne S. Robinson
- Dept. of Chemical and Biomolecular Engineering; Tulane University; New Orleans LA 70118
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Pandey A, Shin K, Patterson RE, Liu XQ, Rainey JK. Current strategies for protein production and purification enabling membrane protein structural biology. Biochem Cell Biol 2016; 94:507-527. [PMID: 27010607 PMCID: PMC5752365 DOI: 10.1139/bcb-2015-0143] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Membrane proteins are still heavily under-represented in the protein data bank (PDB), owing to multiple bottlenecks. The typical low abundance of membrane proteins in their natural hosts makes it necessary to overexpress these proteins either in heterologous systems or through in vitro translation/cell-free expression. Heterologous expression of proteins, in turn, leads to multiple obstacles, owing to the unpredictability of compatibility of the target protein for expression in a given host. The highly hydrophobic and (or) amphipathic nature of membrane proteins also leads to challenges in producing a homogeneous, stable, and pure sample for structural studies. Circumventing these hurdles has become possible through the introduction of novel protein production protocols; efficient protein isolation and sample preparation methods; and, improvement in hardware and software for structural characterization. Combined, these advances have made the past 10-15 years very exciting and eventful for the field of membrane protein structural biology, with an exponential growth in the number of solved membrane protein structures. In this review, we focus on both the advances and diversity of protein production and purification methods that have allowed this growth in structural knowledge of membrane proteins through X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and cryo-electron microscopy (cryo-EM).
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Affiliation(s)
- Aditya Pandey
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Kyungsoo Shin
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Robin E. Patterson
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Xiang-Qin Liu
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Jan K. Rainey
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
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7
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Shiroishi M, Moriya M, Ueda T. Micro-scale and rapid expression screening of highly expressed and/or stable membrane protein variants in Saccharomyces cerevisiae. Protein Sci 2016; 25:1863-72. [PMID: 27479358 DOI: 10.1002/pro.2993] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 06/16/2016] [Accepted: 07/29/2016] [Indexed: 11/07/2022]
Abstract
Purification of milligram quantities of target proteins is required for structural and biophysical studies. However, mammalian membrane proteins, many of which are important therapeutic targets, are too unstable to be expressed in heterologous hosts and to be solubilized by detergents. One of the most promising ways to overcome these limitations is to stabilize the membrane proteins by generating variants via introduction of truncated flexible regions, fusion partners, and site-directed mutagenesis. Therefore, an effective screening strategy is a key to obtaining successful protein stabilization. Herein, we report the micro-scale and high-throughput screening of stabilized membrane protein variants using Saccharomyces cerevisiae as a host. All steps of the screening, including cultivation and disruption of cells, solubilization of the target protein, and the pretreatment for fluorescence-detected size exclusion chromatography (FSEC), could be performed in a 96-well microplate format. We demonstrated that the dispersion among wells was small, enabling detection of a small but important improvement in the protein stability. We also demonstrated that the thermally stable mutants of a human G protein-coupled receptor could be distinguished based on an increase of the peak height in the FSEC profile, which was well correlated with increased ligand binding activity of the protein. This strategy represents a significant platform for handling numerous mutants, similar to alanine scanning.
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Affiliation(s)
- Mitsunori Shiroishi
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-Ku, Fukuoka, 812-8582, Japan.
| | - Mai Moriya
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-Ku, Fukuoka, 812-8582, Japan
| | - Tadashi Ueda
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-Ku, Fukuoka, 812-8582, Japan
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8
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Suharni, Nomura Y, Arakawa T, Hino T, Abe H, Nakada-Nakura Y, Sato Y, Iwanari H, Shiroishi M, Asada H, Shimamura T, Murata T, Kobayashi T, Hamakubo T, Iwata S, Nomura N. Proteoliposome-based selection of a recombinant antibody fragment against the human M2 muscarinic acetylcholine receptor. Monoclon Antib Immunodiagn Immunother 2016; 33:378-85. [PMID: 25545206 DOI: 10.1089/mab.2014.0041] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The development of antibodies against human G-protein-coupled receptors (GPCRs) has achieved limited success, which has mainly been attributed to their low stability in a detergent-solubilized state. We herein describe a method that can generally be applied to the selection of phage display libraries with human GPCRs reconstituted in liposomes. A key feature of this approach is the production of biotinylated proteoliposomes that can be immobilized on the surface of streptavidin-coupled microplates or paramagnetic beads and used as a binding target for antibodies. As an example, we isolated a single chain Fv fragment from an immune phage library that specifically binds to the human M2 muscarinic acetylcholine receptor with nanomolar affinity. The selected antibody fragment recognized the GPCR in both detergent-solubilized and membrane-embedded forms, which suggests that it may be a potentially valuable tool for structural and functional studies of the GPCR. The use of proteoliposomes as immunogens and screening bait will facilitate the application of phage display to this difficult class of membrane proteins.
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Affiliation(s)
- Suharni
- 1 Department of Cell Biology, Graduate School of Medicine, Kyoto University , Sakyo-ku, Kyoto, Japan
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9
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Screening of stable G-protein-coupled receptor variants in Saccharomyces cerevisiae. Methods Mol Biol 2015; 1261:159-70. [PMID: 25502199 DOI: 10.1007/978-1-4939-2230-7_9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
G-protein-coupled receptors (GPCRs) are not only the largest protein family, but as a whole, they represent the largest group of therapeutic drug targets. Recent successes in the determination of GPCR structures have relied on the stabilization of receptors to overcome the difficulties in expression and purification. Although a large quantity of purified protein is needed for structural determination, the majority of wild-type GPCRs are too unstable to express and purify on a large scale. Therefore, rapid screening of highly expressed stable receptor "variants" is crucial. It has been demonstrated that fusing green fluorescent protein (GFP) to a target membrane protein facilitates the evaluation of the physical properties of the membrane protein in detergent. Furthermore, the budding yeast Saccharomyces cerevisiae enables rapid construction of an expression vector via its own efficient homologous recombination system. Herein, we describe the protocols for rapid construction and screening of stable GPCR variants using GFP and S. cerevisiae.
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10
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Mizutani K. High-throughput plasmid construction using homologous recombination in yeast: its mechanisms and application to protein production for X-ray crystallography. Biosci Biotechnol Biochem 2015; 79:1-10. [DOI: 10.1080/09168451.2014.952614] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Abstract
Homologous recombination is a system for repairing the broken genomes of living organisms by connecting two DNA strands at their homologous sequences. Today, homologous recombination in yeast is used for plasmid construction as a substitute for traditional methods using restriction enzymes and ligases. This method has various advantages over the traditional method, including flexibility in the position of DNA insertion and ease of manipulation. Recently, the author of this review reported the construction of plasmids by homologous recombination in the methanol-utilizing yeast Pichia pastoris, which is known to be an excellent expression host for secretory proteins and membrane proteins. The method enabled high-throughput construction of expression systems of proteins using P. pastoris; the constructed expression systems were used to investigate the expression conditions of membrane proteins and to perform X-ray crystallography of secretory proteins. This review discusses the mechanisms and applications of homologous recombination, including the production of proteins for X-ray crystallography.
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Affiliation(s)
- Kimihiko Mizutani
- Laboratory of Applied Structural Biology, Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
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11
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Blocker KM, Britton ZT, Naranjo AN, McNeely PM, Young CL, Robinson AS. Recombinant G Protein-Coupled Receptor Expression in Saccharomyces cerevisiae for Protein Characterization. Methods Enzymol 2015; 556:165-83. [DOI: 10.1016/bs.mie.2014.12.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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12
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Analysing the substrate multispecificity of a proton-coupled oligopeptide transporter using a dipeptide library. Nat Commun 2014; 4:2502. [PMID: 24060756 PMCID: PMC3791473 DOI: 10.1038/ncomms3502] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2013] [Accepted: 08/23/2013] [Indexed: 01/26/2023] Open
Abstract
Peptide uptake systems that involve members of the proton-coupled oligopeptide transporter (POT) family are conserved across all organisms. POT proteins have characteristic substrate multispecificity, with which one transporter can recognize as many as 8,400 types of di/tripeptides and certain peptide-like drugs. Here we characterize the substrate multispecificity of Ptr2p, a major peptide transporter of Saccharomyces cerevisiae, using a dipeptide library. The affinities (Ki) of di/tripeptides toward Ptr2p show a wide distribution range from 48 mM to 0.020 mM. This substrate multispecificity indicates that POT family members have an important role in the preferential uptake of vital amino acids. In addition, we successfully establish high performance ligand affinity prediction models (97% accuracy) using our comprehensive dipeptide screening data in conjunction with simple property indices for describing ligand molecules. Our results provide an important clue to the development of highly absorbable peptides and their derivatives including peptide-like drugs. Proton-coupled oligopeptide transporters (POTs) can recognize and mediate the uptake of up to 8,400 di/tripeptides or peptide-like drugs. Ito et al. comprehensively map the substrate specificity of the yeast POT Ptr2p, and use this information to construct models for the prediction of ligand affinity.
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Lan VTT, Ito K, Ito S, Kawarasaki Y. Trp-Arg-Xaa tripeptides act as uncompetitive-type inhibitors of human dipeptidyl peptidase IV. Peptides 2014; 54:166-70. [PMID: 24512990 DOI: 10.1016/j.peptides.2014.01.027] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 01/30/2014] [Accepted: 01/30/2014] [Indexed: 12/23/2022]
Abstract
Human dipeptidyl peptidase IV (hDPPIV, alternative name: CD26) inhibitors provide an effective strategy for the treatment of type 2 diabetes. Recently, our research group discovered a non substrate-mimic inhibitory dipeptide, Trp-Arg, by the systematic analysis of a dipeptide library. In the present study, a tripeptide library Trp-Arg-Xaa (where Xaa represents any amino acid) was analyzed to investigate the interactions of peptidergic inhibitors with hDPPIV. Trp-Arg-Glu showed the highest inhibitory effect toward hDPPIV (Ki=130 μM). All of the tested 19 Trp-Arg-Xaa tripeptides showed unique uncompetitive-type inhibition. The inhibition mechanism of Trp-Arg-Xaa is discussed based on the crystal structure of hDPPIV. The information obtained by this study suggests a novel concept for developing hDPPIV inhibitory peptides and drugs.
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Affiliation(s)
- Vu Thi Tuyet Lan
- Graduate School of Nutritional and Environmental Sciences, University of Shizuoka, Yada 52-1, Suruga-ku, Shizuoka 422-8526, Japan
| | - Keisuke Ito
- Graduate School of Nutritional and Environmental Sciences, University of Shizuoka, Yada 52-1, Suruga-ku, Shizuoka 422-8526, Japan.
| | - Sohei Ito
- Graduate School of Nutritional and Environmental Sciences, University of Shizuoka, Yada 52-1, Suruga-ku, Shizuoka 422-8526, Japan
| | - Yasuaki Kawarasaki
- Graduate School of Nutritional and Environmental Sciences, University of Shizuoka, Yada 52-1, Suruga-ku, Shizuoka 422-8526, Japan
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The anaphase promoting complex regulates yeast lifespan and rDNA stability by targeting Fob1 for degradation. Genetics 2013; 196:693-709. [PMID: 24361936 DOI: 10.1534/genetics.113.158949] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Genomic stability, stress response, and nutrient signaling all play critical, evolutionarily conserved roles in lifespan determination. However, the molecular mechanisms coordinating these processes with longevity remain unresolved. Here we investigate the involvement of the yeast anaphase promoting complex (APC) in longevity. The APC governs passage through M and G1 via ubiquitin-dependent targeting of substrate proteins and is associated with cancer and premature aging when defective. Our two-hybrid screen utilizing Apc5 as bait recovered the lifespan determinant Fob1 as prey. Fob1 is unstable specifically in G1, cycles throughout the cell cycle in a manner similar to Clb2 (an APC target), and is stabilized in APC (apc5(CA)) and proteasome (rpn10) mutants. Deletion of FOB1 increased replicative lifespan (RLS) in wild type (WT), apc5(CA), and apc10 cells, and suppressed apc5(CA) cell cycle progression and rDNA recombination defects. Alternatively, increased FOB1 expression decreased RLS in WT cells, but did not reduce the already short apc5(CA) RLS, suggesting an epistatic interaction between apc5(CA) and fob1. Mutation to a putative L-Box (Fob1(E420V)), a Destruction Box-like motif, abolished Fob1 modifications, stabilized the protein, and increased rDNA recombination. Our work provides a mechanistic role played by the APC to promote replicative longevity and genomic stability in yeast.
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15
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Hikida A, Ito K, Motoyama T, Kato R, Kawarasaki Y. Systematic analysis of a dipeptide library for inhibitor development using human dipeptidyl peptidase IV produced by a Saccharomyces cerevisiae expression system. Biochem Biophys Res Commun 2013; 430:1217-22. [DOI: 10.1016/j.bbrc.2012.12.073] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2012] [Accepted: 12/18/2012] [Indexed: 02/06/2023]
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16
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Grey JL, Thompson DH. Challenges and opportunities for new protein crystallization strategies in structure-based drug design. Expert Opin Drug Discov 2012; 5:1039-45. [PMID: 21116481 DOI: 10.1517/17460441.2010.515583] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Structure-based drug design (SBDD) has emerged as a valuable pharmaceutical lead discovery tool, showing potential for accelerating the discovery process,while reducing developmental costs and boosting potencies of the drug that is ultimately selected. SBDD is an iterative, rational, lead compound sculpting process that involves both the synthesis of new derivatives and the evaluation of their binding to the target structure either through computational docking or elucidation of the target structure as a complex with the lead compound. This method heavily relies on the production of high resolution(< 2 Å) 3D structures of the drug target, obtained through X-ray crystallographic analysis, in the presence or absence of the drug candidate.The lack of generalized methods for high quality crystal production is still a major bottleneck in the process of macromolecular crystallization. This review provides a brief introduction to SBDD and describes several macromolecular crystallization strategies, with an emphasis on advances and challenges facing researchers in the field today. Recent trends in the development of more universal macromolecular crystallization techniques, particularly nucleation-based techniques that are applicable to both soluble and integral membrane proteins, are also discussed.
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Affiliation(s)
- Jessica Lynn Grey
- Purdue University, Department of Chemistry, West Lafayette, IN 47907, USA
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17
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Hara K, Shigemori T, Kuroda K, Ueda M. Membrane-displayed somatostatin activates somatostatin receptor subtype-2 heterologously produced in Saccharomyces cerevisiae. AMB Express 2012. [PMID: 23193953 PMCID: PMC3558460 DOI: 10.1186/2191-0855-2-63] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The G-protein-coupled receptor (GPCR) superfamily, which includes somatostatin receptors (SSTRs), is one of the most important drug targets in the pharmaceutical industry. The yeast Saccharomyces cerevisiae is an attractive host for the ligand screening of human GPCRs. Here, we demonstrate the utility of the technology that was developed for displaying peptide ligands on yeast plasma membrane, termed "PepDisplay", which triggers signal transduction upon GPCR activation. A yeast strain that heterologously produced human somatostatin receptor subtype-2 (SSTR2) and chimeric Gα protein was constructed along with membrane-displayed somatostatin; somatostatin was displayed on the yeast plasma membrane by linking it to the anchoring domain of the glycosylphosphatidylinositol anchored plasma membrane protein Yps1p. We demonstrate that the somatostatin displayed on the plasma membrane successfully activated human SSTR2 in S. cerevisiae. The methodology presented here provides a new platform for identifying novel peptide ligands for both liganded and orphan mammalian GPCRs.
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Soy peptides enhance heterologous membrane protein productivity during the exponential growth phase of Saccharomyces cerevisiae. Biosci Biotechnol Biochem 2012; 76:628-31. [PMID: 22451416 DOI: 10.1271/bbb.110965] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
In this study, the production of eight G protein-coupled receptors by Saccharomyces cerevisiae was compared using two types of media, one of which contained soy peptides and the other free amino acids. Yeast cell growth improved in the medium with soy peptides, and the expression levels of six of the receptors increased during the exponential phase by an average of 2.3-fold as against the free amino acid-based medium. The enhancement of protein expression by soy peptides can be explained by alleviation of metabolite stress due to amino acid source depletion caused by heterologous protein expression.
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Shiroishi M, Tsujimoto H, Makyio H, Asada H, Yurugi-Kobayashi T, Shimamura T, Murata T, Nomura N, Haga T, Iwata S, Kobayashi T. Platform for the rapid construction and evaluation of GPCRs for crystallography in Saccharomyces cerevisiae. Microb Cell Fact 2012; 11:78. [PMID: 22694812 PMCID: PMC3495400 DOI: 10.1186/1475-2859-11-78] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Accepted: 06/13/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Recent successes in the determination of G-protein coupled receptor (GPCR) structures have relied on the ability of receptor variants to overcome difficulties in expression and purification. Therefore, the quick screening of functionally expressed stable receptor variants is vital. RESULTS We developed a platform using Saccharomyces cerevisiae for the rapid construction and evaluation of functional GPCR variants for structural studies. This platform enables us to perform a screening cycle from construction to evaluation of variants within 6-7 days. We firstly confirmed the functional expression of 25 full-length class A GPCRs in this platform. Then, in order to improve the expression level and stability, we generated and evaluated the variants of the four GPCRs (hADRB2, hCHRM2, hHRH1 and hNTSR1). These stabilized receptor variants improved both functional activity and monodispersity. Finally, the expression level of the stabilized hHRH1 in Pichia pastoris was improved up to 65 pmol/mg from negligible expression of the functional full-length receptor in S. cerevisiae at first screening. The stabilized hHRH1 was able to be purified for use in crystallization trials. CONCLUSIONS We demonstrated that the S. cerevisiae system should serve as an easy-to-handle and rapid platform for the construction and evaluation of GPCR variants. This platform can be a powerful prescreening method to identify a suitable GPCR variant for crystallography.
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Affiliation(s)
- Mitsunori Shiroishi
- Iwata Human Receptor Crystallography project, ERATO, JST, Kyoto 606-8501, Japan.
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Shiroishi M, Kobayashi T, Ogasawara S, Tsujimoto H, Ikeda-Suno C, Iwata S, Shimamura T. Production of the stable human histamine H₁ receptor in Pichia pastoris for structural determination. Methods 2011; 55:281-6. [PMID: 21903167 DOI: 10.1016/j.ymeth.2011.08.015] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2011] [Revised: 08/21/2011] [Accepted: 08/22/2011] [Indexed: 12/15/2022] Open
Abstract
G-protein coupled receptors (GPCRs) play essential roles in regulation of many physiological processes and are one of the major targets of pharmaceutical drugs. The 3D structure can provide important information for the understanding of GPCR function and the design of new drugs. However, the success of structure determination relies largely on the production of recombinant GPCRs, because the expression levels of GPCRs are very low in native tissues except rhodopsin. All non-rhodopsin GPCRs whose structures were determined so far were expressed in insect cells and the availability of other hosts was unknown. Recently, we succeeded to determine the structure of human histamine H(1) receptor (H(1)R) expressed in Pichia pastoris. Here, we report the expression and purification procedures of recombinant H(1)R used in the structural determination. The receptor was designed to possess a N-terminal 19-residue deletion and a replacement of the third cytoplasmic loop with T4-lysozyme. The receptor was verified to show similar binding activities with the receptor expressed in other hosts. The receptor was purified by the immobilized metal ion affinity chromatography and used for the crystallographic study that resulted in the successful structure determination.
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Affiliation(s)
- Mitsunori Shiroishi
- Human Receptor Crystallography Project, ERATO, Japan Science and Technology Agency, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
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Mizutani K, Yoshioka S, Mizutani Y, Iwata S, Mikami B. High-throughput construction of expression system using yeast Pichia pastoris, and its application to membrane proteins. Protein Expr Purif 2011; 77:1-8. [DOI: 10.1016/j.pep.2010.12.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Revised: 12/14/2010] [Accepted: 12/14/2010] [Indexed: 12/01/2022]
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Cysteine-to-serine shuffling using a Saccharomyces cerevisiae expression system improves protein secretion: case of a nonglycosylated mutant of miraculin, a taste-modifying protein. Biotechnol Lett 2010; 33:103-7. [PMID: 20936326 DOI: 10.1007/s10529-010-0399-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Accepted: 08/27/2010] [Indexed: 10/19/2022]
Abstract
PURPOSE OF WORK Soluble protein expression is an important first step during various types of protein studies. Here, we present the screening strategy of secretable mutant. The strategy aimed to identify those cysteine residues that provoke protein misfolding in the heterologous expression system. Intentional mutagenesis studies should consider the size of the library and the time required for expression screening. Here, we proposed a cysteine-to-serine shuffling mutation strategy (CS shuffling) using a Saccharomyces cerevisiae expression system. This strategy of site-directed shuffling mutagenesis of cysteine-to-serine residues aims to identify the cysteine residues that cause protein misfolding in heterologous expression. In the case of a nonglycosylated mutant of the taste-modifying protein miraculin (MCL), which was used here as a model protein, 25% of all constructs obtained from CS shuffling expressed MCL mutant, and serine mutations were found at Cys47 or Cys92, which are involved in the formation of the disulfide bond. This indicates that these residues had the potential to provoke protein misfolding via incorrect disulfide bonding. The CS shuffling can be performed using a small library and within one week, and is an effective screening strategy of soluble protein expression.
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Bulky high-mannose-type N-glycan blocks the taste-modifying activity of miraculin. Biochim Biophys Acta Gen Subj 2010; 1800:986-92. [DOI: 10.1016/j.bbagen.2010.06.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Revised: 05/17/2010] [Accepted: 06/04/2010] [Indexed: 11/20/2022]
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Freigassner M, Pichler H, Glieder A. Tuning microbial hosts for membrane protein production. Microb Cell Fact 2009; 8:69. [PMID: 20040113 PMCID: PMC2807855 DOI: 10.1186/1475-2859-8-69] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2009] [Accepted: 12/29/2009] [Indexed: 12/22/2022] Open
Abstract
The last four years have brought exciting progress in membrane protein research. Finally those many efforts that have been put into expression of eukaryotic membrane proteins are coming to fruition and enable to solve an ever-growing number of high resolution structures. In the past, many skilful optimization steps were required to achieve sufficient expression of functional membrane proteins. Optimization was performed individually for every membrane protein, but provided insight about commonly encountered bottlenecks and, more importantly, general guidelines how to alleviate cellular limitations during microbial membrane protein expression. Lately, system-wide analyses are emerging as powerful means to decipher cellular bottlenecks during heterologous protein production and their use in microbial membrane protein expression has grown in popularity during the past months. This review covers the most prominent solutions and pitfalls in expression of eukaryotic membrane proteins using microbial hosts (prokaryotes, yeasts), highlights skilful applications of our basic understanding to improve membrane protein production. Omics technologies provide new concepts to engineer microbial hosts for membrane protein production.
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Affiliation(s)
- Maria Freigassner
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria.
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Koth CMM, Payandeh J. Strategies for the cloning and expression of membrane proteins. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2009; 76:43-86. [PMID: 20663478 DOI: 10.1016/s1876-1623(08)76002-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Despite the determination of thousands of high-resolution structures of soluble proteins, many features of integral membrane proteins render them difficult targets for the structural biologist. Among these, the most important challenge is in expressing sufficient quantities of active protein to support downstream purification and structure determination efforts. Over 190 unique membrane protein structures have now been solved, and noticeable trends in successful expression strategies are beginning to emerge. A number of groups have also explored high-throughput (HTP) methods for membrane protein expression, with varying degrees of success. Here we review the current state of expressing membrane proteins for functional and structural studies. We first survey successful methods that have already yielded levels of membrane protein expression sufficient for structure determination. HTP methods are also examined since these aim to explore large numbers of targets and can predict reasonable starting points for many membrane proteins. Since HTP techniques may fail, particularly for certain classes of eukaryotic targets, detailed strategies for the expression of two prominent classes of eukaryotic protein families, G-protein-coupled receptors and ion channels, are also summarized.
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Affiliation(s)
- Christopher M M Koth
- Department of Structural Biology, Genentech, South San Francisco, California 94080, USA
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Sugawara T, Ito K, Shiroishi M, Tokuda N, Asada H, Yurugi-Kobayashi T, Shimamura T, Misaka T, Nomura N, Murata T, Abe K, Iwata S, Kobayashi T. Fluorescence-based optimization of human bitter taste receptor expression in Saccharomyces cerevisiae. Biochem Biophys Res Commun 2009; 382:704-10. [DOI: 10.1016/j.bbrc.2009.03.089] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2009] [Accepted: 03/17/2009] [Indexed: 10/21/2022]
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Ciciriello F, Costanzo G, Pino S, Di Mauro E. Spontaneous Generation Revisited at the Molecular Level. Evol Biol 2009. [DOI: 10.1007/978-3-642-00952-5_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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