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Gimenez LE, Martin C, Yu J, Hollanders C, Hernandez CC, Wu Y, Yao D, Han GW, Dahir NS, Wu L, Van der Poorten O, Lamouroux A, Mannes M, Zhao S, Tourwé D, Stevens RC, Cone RD, Ballet S. Novel Cocrystal Structures of Peptide Antagonists Bound to the Human Melanocortin Receptor 4 Unveil Unexplored Grounds for Structure-Based Drug Design. J Med Chem 2024; 67:2690-2711. [PMID: 38345933 DOI: 10.1021/acs.jmedchem.3c01822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Melanocortin 4 receptor (MC4-R) antagonists are actively sought for treating cancer cachexia. We determined the structures of complexes with PG-934 and SBL-MC-31. These peptides differ from SHU9119 by substituting His6 with Pro6 and inserting Gly10 or Arg10. The structures revealed two subpockets at the TM7-TM1-TM2 domains, separated by N2857.36. Two peptide series based on the complexed peptides led to an antagonist activity and selectivity SAR study. Most ligands retained the SHU9119 potency, but several SBL-MC-31-derived peptides significantly enhanced MC4-R selectivity over MC1-R by 60- to 132-fold. We also investigated MC4-R coupling to the K+ channel, Kir7.1. Some peptides activated the channel, whereas others induced channel closure independently of G protein coupling. In cell culture studies, channel activation correlated with increased feeding, while a peptide with Kir7.1 inhibitory activity reduced eating. These results highlight the potential for targeting the MC4-R:Kir7.1 complex for treating positive and restrictive eating disorders.
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Affiliation(s)
- Luis E Gimenez
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Charlotte Martin
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, Brussels B-1050, Belgium
| | - Jing Yu
- iHuman Institute, ShanghaiTech University, Ren Building, 393 Middle Huaxia Road, Pudong, Shanghai 201210, China
| | - Charlie Hollanders
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, Brussels B-1050, Belgium
| | - Ciria C Hernandez
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Yiran Wu
- iHuman Institute, ShanghaiTech University, Ren Building, 393 Middle Huaxia Road, Pudong, Shanghai 201210, China
| | - Deqiang Yao
- iHuman Institute, ShanghaiTech University, Ren Building, 393 Middle Huaxia Road, Pudong, Shanghai 201210, China
| | - Gye Won Han
- Departments of Biological Sciences and Chemistry, Bridge Institute, USC Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, United States
| | - Naima S Dahir
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Molecular and Integrative Physiology, School of Medicine, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Lijie Wu
- iHuman Institute, ShanghaiTech University, Ren Building, 393 Middle Huaxia Road, Pudong, Shanghai 201210, China
| | - Olivier Van der Poorten
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, Brussels B-1050, Belgium
| | - Arthur Lamouroux
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, Brussels B-1050, Belgium
| | - Morgane Mannes
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, Brussels B-1050, Belgium
| | - Suwen Zhao
- iHuman Institute, ShanghaiTech University, Ren Building, 393 Middle Huaxia Road, Pudong, Shanghai 201210, China
| | - Dirk Tourwé
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, Brussels B-1050, Belgium
| | - Raymond C Stevens
- iHuman Institute, ShanghaiTech University, Ren Building, 393 Middle Huaxia Road, Pudong, Shanghai 201210, China
| | - Roger D Cone
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Molecular and Integrative Physiology, School of Medicine, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Molecular, Cellular, and Developmental Biology, College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Steven Ballet
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, Brussels B-1050, Belgium
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2
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Dmitrieva DA, Kotova TV, Safronova NA, Sadova AA, Dashevskii DE, Mishin AV. Protein Design Strategies for the Structural–Functional Studies of G Protein-Coupled Receptors. BIOCHEMISTRY (MOSCOW) 2023; 88:S192-S226. [PMID: 37069121 DOI: 10.1134/s0006297923140110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
G protein-coupled receptors (GPCRs) are an important family of membrane proteins responsible for many physiological functions in human body. High resolution GPCR structures are required to understand their molecular mechanisms and perform rational drug design, as GPCRs play a crucial role in a variety of diseases. That is difficult to obtain for the wild-type proteins because of their low stability. In this review, we discuss how this problem can be solved by using protein design strategies developed to obtain homogeneous stabilized GPCR samples for crystallization and cryoelectron microscopy.
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Affiliation(s)
- Daria A Dmitrieva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Tatiana V Kotova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Nadezda A Safronova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Alexandra A Sadova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Dmitrii E Dashevskii
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Alexey V Mishin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.
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3
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Xue J, Zhang H, Zeng S. Integrate thermostabilized fusion protein apocytochrome b562RIL and N-glycosylation mutations: A novel approach to heterologous expression of human UDP-glucuronosyltransferase (UGT) 2B7. Front Pharmacol 2022; 13:965038. [PMID: 36034790 PMCID: PMC9412022 DOI: 10.3389/fphar.2022.965038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 07/19/2022] [Indexed: 11/15/2022] Open
Abstract
Human UDP-glucuronosyltransferase (UGT) 2B7 is a crucial phase II metabolic enzyme that transfers glucuronic acid from UDP-glucuronic acid (UDPGA) to endobiotic and xenobiotic substrates. Biophysical and biochemical investigations of UGT2B7 are hampered by the challenge of the integral membrane protein purification. This study focused on the expression and purification of recombinant UGT2B7 by optimizing the insertion sites for the thermostabilized fusion protein apocytochrome b562RIL (BRIL) and various mutations to improve the protein yields and homogeneity. Preparation of the recombinant proteins with high purity accelerated the measurement of pharmacokinetic parameters of UGT2B7. The dissociation constants (KD) of two classical substrates (zidovudine and androsterone) and two inhibitors (schisanhenol and hesperetin) of UGT2B7 were determined using the surface plasmon resonance spectroscopy (SPR) for the first time. Using negative-staining transmission electron microscopy (TEM), UGT2B7 protein particles were characterized, which could be useful for further exploring its three-dimensional structure. The methods described in this study could be broadly applied to other UGTs and are expected to provide the basis for the exploration of metabolic enzyme kinetics, the mechanisms of drug metabolisms and drug interactions, changes in pharmacokinetics, and pharmacodynamics studies in vitro.
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Affiliation(s)
- Jia Xue
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Haitao Zhang
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Hangzhou Institute of Innovative Medicine, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- *Correspondence: Haitao Zhang, ; Su Zeng,
| | - Su Zeng
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- *Correspondence: Haitao Zhang, ; Su Zeng,
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4
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Schöppe J, Ehrenmann J, Waltenspühl Y, Plückthun A. Universal platform for the generation of thermostabilized GPCRs that crystallize in LCP. Nat Protoc 2022; 17:698-726. [PMID: 35140409 DOI: 10.1038/s41596-021-00660-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 11/08/2021] [Indexed: 12/13/2022]
Abstract
Structural studies of G-protein-coupled receptors (GPCRs) are often limited by difficulties in obtaining well-diffracting crystals suitable for high-resolution structure determination. During the past decade, crystallization in lipidic cubic phase (LCP) has become the most successful and widely used technique for obtaining such crystals. Despite often intense efforts, many GPCRs remain refractory to crystallization, even if receptors can be purified in sufficient amounts. To address this issue, we have developed a highly efficient screening and stabilization strategy for GPCRs, based on a fluorescence thermal stability assay readout, which seems to correlate particularly well with those GPCR constructs that remain native during incorporation into the LCP. Detailed protocols are provided for rapid and cost-efficient mutant and construct generation using sequence- and ligation-independent cloning, high-throughput magnetic bead-based protein purification from small-scale expressions in mammalian cells, the screening and optimal combination of mutations for increased receptor thermostability and the rapid identification of suitable chimeric fusion protein constructs for successful crystallization in LCP. We exemplify the method on three receptors from two different classes: the neurokinin 1 receptor, the oxytocin receptor and the parathyroid hormone 1 receptor.
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Affiliation(s)
- Jendrik Schöppe
- Department of Biochemistry, University of Zürich, Zurich, Switzerland.,Novo Nordisk A/S, Måløv, Denmark
| | - Janosch Ehrenmann
- Department of Biochemistry, University of Zürich, Zurich, Switzerland.,leadXpro AG, PARK InnovAARE, Villigen, Switzerland
| | - Yann Waltenspühl
- Department of Biochemistry, University of Zürich, Zurich, Switzerland
| | - Andreas Plückthun
- Department of Biochemistry, University of Zürich, Zurich, Switzerland.
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5
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Li X, Shen L, Liu J, Liu X, Liu ZJ, Hua T. Heterologous Expression and Purification of GPCRs. Methods Mol Biol 2022; 2507:295-312. [PMID: 35773588 DOI: 10.1007/978-1-0716-2368-8_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
G protein-coupled receptors (GPCRs) are involved in a variety of human physiological processes and are attractive targets for treating various diseases. Yet, despite the importance as therapeutic targets, only 97 unique GPCR structures have been determined to date. A key challenge in their structural biology study is to obtain adequate protein samples because GPCRs usually have the low expression in native tissues. The in vitro recombinant expression provides the possibility to obtain large quantities of high-quality proteins suitable for three-dimensional structure determination by crystallography or single particle cryo-EM methods. For GPCR protein production, eukaryotic expression systems, such as baculovirus system and mammalian system, are the most widely used. In this chapter, we provide an overview of the methodological approaches on GPCRs expression and purification optimization using insect cells and mammalian cells, which is the prerequisite conditions for structural biology studies.
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Affiliation(s)
- Xiaoting Li
- iHuman Institute, ShanghaiTech University, Shanghai, China
| | - Ling Shen
- iHuman Institute, ShanghaiTech University, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Junlin Liu
- iHuman Institute, ShanghaiTech University, Shanghai, China
| | - Xiaoyan Liu
- iHuman Institute, ShanghaiTech University, Shanghai, China
| | - Zhi-Jie Liu
- iHuman Institute, ShanghaiTech University, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Tian Hua
- iHuman Institute, ShanghaiTech University, Shanghai, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
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6
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Qi M, Liu X, Zhou Y, Wang H, Zhao Y, Ren J, Xiang J. Berberine Inhibits MDA-MB-231 Cells as an Agonist of G Protein-Coupled Estrogen Receptor 1. Int J Mol Sci 2021; 22:ijms222111466. [PMID: 34768896 PMCID: PMC8583996 DOI: 10.3390/ijms222111466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/15/2021] [Accepted: 10/19/2021] [Indexed: 01/18/2023] Open
Abstract
G protein-coupled estrogen receptor 1 (GPER1) is a potential therapeutic target for treating triple-negative breast cancers (TNBC). However, modulators for GPER1 that can be used to treat TNBC have not appeared. Berberine (BBR) is a bioactive isoquinoline alkaloid with high oral safety. In recent years, BBR has shown an inhibitory effect on TNBC tumors such as MDA-MB-231, but the molecular target remains unclear, which hinders related clinical research. Our work proved that BBR is a modulator of GPER1 that can inhibit cell viability, migration, and autophagy of MDA-MB-231 cells. The inhibitory effect of BBR on MDA-MB-231 cells has a dependence on estrogen levels. Although BBR promoted the proteasome, which is a major factor in the degradation of GPER1, it could still induce the protein level of GPER1. Correspondingly, the transcription of cellular communication network factor 2 (CCN2) was promoted. BBR could bind to GPER1 directly and change the secondary structure of GPER1, as in the case of 17β-estradiol (E2). In addition, BBR induced not only a high degree of co-localization of GPER1 and microtubule-associated protein 1 light chain 3 (MAP1LC3), but also the accumulation of sequestosome 1 (SQSTM1/p62) by the inhibition of the nuclear translocation of the nuclear factor-kappa B (NF-κB) subunit (RELA/p65), which indicates NF-κB inhibition and anti-cancer effects. This result proved that the promotional effect of BBR on the GPER1/NF-κB pathway was closely related to its inhibitory effect on autophagy, which may serve as a new mechanism by which to explain the inhibitory effect of BBR on MDA-MB-231 cells and expand our understanding of the function of both BBR and GPER1.
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Affiliation(s)
- Miaomiao Qi
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China; (M.Q.); (X.L.); (H.W.); (Y.Z.); (J.R.)
| | - Xiang Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China; (M.Q.); (X.L.); (H.W.); (Y.Z.); (J.R.)
| | - Ying Zhou
- Research Center for Medicine and Structural Biology of Wuhan University, Wuhan University, Wuhan 430071, China;
| | - Haoyu Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China; (M.Q.); (X.L.); (H.W.); (Y.Z.); (J.R.)
| | - Ying Zhao
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China; (M.Q.); (X.L.); (H.W.); (Y.Z.); (J.R.)
| | - Jing Ren
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China; (M.Q.); (X.L.); (H.W.); (Y.Z.); (J.R.)
| | - Jin Xiang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China; (M.Q.); (X.L.); (H.W.); (Y.Z.); (J.R.)
- Correspondence:
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7
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Yeliseev AA, Zoretich K, Hooper L, Teague W, Zoubak L, Hines KG, Gawrisch K. Site-selective labeling and electron paramagnetic resonance studies of human cannabinoid receptor CB 2. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2021; 1863:183621. [PMID: 33865808 PMCID: PMC8154700 DOI: 10.1016/j.bbamem.2021.183621] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 03/19/2021] [Accepted: 03/26/2021] [Indexed: 11/19/2022]
Abstract
Integral membrane G protein-coupled receptors (GPCR) regulate multiple physiological processes by transmitting signals from extracellular milieu to intracellular proteins and are major targets of pharmaceutical drug development. Since GPCR are inherently flexible proteins, their conformational dynamics can be studied by spectroscopic techniques such as electron paramagnetic resonance (EPR) which requires selective chemical labeling of the protein. Here, we developed protocols for selective chemical labeling of the recombinant human cannabinoid receptor CB2 by judiciously replacing naturally occurring reactive cysteine residues and introducing a new single cysteine residue in selected positions. The majority of the 47 newly generated single cysteine constructs expressed well in E. coli cells, and more than half of them retained high functional activity. The reactivity of newly introduced cysteine residues was assessed by incorporating nitroxide spin label and EPR measurement. The conformational transition of the receptor between the inactive and activated form were studied by EPR of selectively labeled constructs in the presence of either a full agonist CP-55,940 or an inverse agonist SR-144,528. We observed evidence for higher mobility of labels in the center of internal loop 3 and a structural change between agonist vs. inverse agonist-bound CB2 in the extracellular tip of transmembrane helix 6. Our results demonstrate the utility of EPR for studies of conformational dynamics of CB2.
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Affiliation(s)
- Alexei A Yeliseev
- National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Kaeli Zoretich
- National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD 20892, USA
| | - Levi Hooper
- National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD 20892, USA
| | - Walter Teague
- National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lioudmila Zoubak
- National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kirk G Hines
- National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD 20892, USA
| | - Klaus Gawrisch
- National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD 20892, USA.
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8
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Morimoto K. [Activation Mechanism of Prostanoid Receptors -X-ray Crystallography of EP3 Receptor]. YAKUGAKU ZASSHI 2021; 141:473-479. [PMID: 33790113 DOI: 10.1248/yakushi.20-00202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Prostanoids [prostaglandins (PGs) and thromboxanes (TXs)] are a series of bioactive lipid metabolites that function in an autacoid manner via activation of cognate G protein-coupled receptors (GPCRs). The nine subtypes of prostanoid receptors (DP1, DP2, EP1, EP2, EP3, EP4, FP, IP, TP) are involved in a wide range of functions, including inflammation, immune response, reproduction, and homeostasis of the intestinal mucosa and cardiovascular system. Among the prostanoid receptors, the structure of antagonist-bound DP2, which belongs to the chemoattractant receptor family, was previously determined. However, the mechanisms of prostanoid recognition and receptor activation remained elusive. To address this issue, we determined the crystal structures of antagonist-bound EP4 and PGE2-bound EP3. The EP3-PGE2 complex exhibits an active-like conformation, including outward movement of the cytoplasmic end of transmembrane (TM) 6 relative to the cytoplasmic end of TM6 of the EP4 complex. The carboxyl moiety of PGE2 is recognized through three hydrogen bonds formed by highly conserved residues: Y1142.65, T206Extracelluar loop 2 (ECL2), and R3337.40 (superscripts denote Ballesteros-Weinstein numbering). In addition, the ω-chain of PGE2 orients toward TM6, which appears to contribute to receptor activation. The structure reveals important insights into the activation mechanism of prostanoid receptors and provides a molecular basis for the binding modes of endogenous ligands. These findings should facilitate the development of subtype-selective and non-PG-like ligands.
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Affiliation(s)
- Kazushi Morimoto
- Department of Cell Biology, Graduate School of Medicine, Kyoto University
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9
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Structural Characterization of Receptor-Receptor Interactions in the Allosteric Modulation of G Protein-Coupled Receptor (GPCR) Dimers. Int J Mol Sci 2021; 22:ijms22063241. [PMID: 33810175 PMCID: PMC8005122 DOI: 10.3390/ijms22063241] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/17/2021] [Accepted: 03/20/2021] [Indexed: 01/07/2023] Open
Abstract
G protein-coupled receptor (GPCR) oligomerization, while contentious, continues to attract the attention of researchers. Numerous experimental investigations have validated the presence of GPCR dimers, and the relevance of dimerization in the effectuation of physiological functions intensifies the attractiveness of this concept as a potential therapeutic target. GPCRs, as a single entity, have been the main source of scrutiny for drug design objectives for multiple diseases such as cancer, inflammation, cardiac, and respiratory diseases. The existence of dimers broadens the research scope of GPCR functions, revealing new signaling pathways that can be targeted for disease pathogenesis that have not previously been reported when GPCRs were only viewed in their monomeric form. This review will highlight several aspects of GPCR dimerization, which include a summary of the structural elucidation of the allosteric modulation of class C GPCR activation offered through recent solutions to the three-dimensional, full-length structures of metabotropic glutamate receptor and γ-aminobutyric acid B receptor as well as the role of dimerization in the modification of GPCR function and allostery. With the growing influence of computational methods in the study of GPCRs, we will also be reviewing recent computational tools that have been utilized to map protein-protein interactions (PPI).
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10
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Heim B, Handrick R, Hartmann MD, Kiefer H. Refolding and characterization of two G protein-coupled receptors purified from E. coli inclusion bodies. PLoS One 2021; 16:e0247689. [PMID: 33626080 PMCID: PMC7904181 DOI: 10.1371/journal.pone.0247689] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 02/10/2021] [Indexed: 11/18/2022] Open
Abstract
Aiming at streamlining GPCR production from E. coli inclusion bodies for structural analysis, we present a generic approach to assess and optimize refolding yield through thermostability analysis. Since commonly used hydrophobic dyes cannot be applied as probes for membrane protein unfolding, we adapted a technique based on reacting cysteins exposed upon thermal denaturation with fluorescent 7-Diethylamino-3-(4-maleimidophenyl)-4-methylcoumarin (CPM). Successful expression, purification and refolding is shown for two G protein-coupled receptors (GPCR), the sphingosine-1-phosphate receptor S1P1, and the orphan receptor GPR3. Refolded receptors were subjected to lipidic cubic phase crystallization screening.
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Affiliation(s)
- Bastian Heim
- Institute of Applied Biotechnology, University of Applied Sciences, Biberach, Germany
- * E-mail:
| | - René Handrick
- Institute of Applied Biotechnology, University of Applied Sciences, Biberach, Germany
| | | | - Hans Kiefer
- Institute of Applied Biotechnology, University of Applied Sciences, Biberach, Germany
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11
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Tiss A, Ben Boubaker R, Henrion D, Guissouma H, Chabbert M. Homology Modeling of Class A G-Protein-Coupled Receptors in the Age of the Structure Boom. Methods Mol Biol 2021; 2315:73-97. [PMID: 34302671 DOI: 10.1007/978-1-0716-1468-6_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
With 700 members, G protein-coupled receptors (GPCRs) of the rhodopsin family (class A) form the largest membrane receptor family in humans and are the target of about 30% of presently available pharmaceutical drugs. The recent boom in GPCR structures led to the structural resolution of 57 unique receptors in different states (39 receptors in inactive state only, 2 receptors in active state only and 16 receptors in different activation states). In spite of these tremendous advances, most computational studies on GPCRs, including molecular dynamics simulations, virtual screening and drug design, rely on GPCR models obtained by homology modeling. In this protocol, we detail the different steps of homology modeling with the MODELLER software, from template selection to model evaluation. The present structure boom provides closely related templates for most receptors. If, in these templates, some of the loops are not resolved, in most cases, the numerous available structures enable to find loop templates with similar length for equivalent loops. However, simultaneously, the large number of putative templates leads to model ambiguities that may require additional information based on multiple sequence alignments or molecular dynamics simulations to be resolved. Using the modeling of the human bradykinin receptor B1 as a case study, we show how several templates are managed by MODELLER, and how the choice of template(s) and of template fragments can improve the quality of the models. We also give examples of how additional information and tools help the user to resolve ambiguities in GPCR modeling.
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Affiliation(s)
- Asma Tiss
- UMR CNRS 6015 - INSERM 1083, Laboratoire MITOVASC, Université d'Angers, Angers, France.,Laboratoire de Génétique, Immunologie et Pathologies Humaines, Département de Biologie, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, Tunisie
| | - Rym Ben Boubaker
- UMR CNRS 6015 - INSERM 1083, Laboratoire MITOVASC, Université d'Angers, Angers, France
| | - Daniel Henrion
- UMR CNRS 6015 - INSERM 1083, Laboratoire MITOVASC, Université d'Angers, Angers, France
| | - Hajer Guissouma
- Laboratoire de Génétique, Immunologie et Pathologies Humaines, Département de Biologie, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, Tunisie
| | - Marie Chabbert
- UMR CNRS 6015 - INSERM 1083, Laboratoire MITOVASC, Université d'Angers, Angers, France.
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12
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Capturing Peptide-GPCR Interactions and Their Dynamics. Molecules 2020; 25:molecules25204724. [PMID: 33076289 PMCID: PMC7587574 DOI: 10.3390/molecules25204724] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/08/2020] [Accepted: 10/09/2020] [Indexed: 12/16/2022] Open
Abstract
Many biological functions of peptides are mediated through G protein-coupled receptors (GPCRs). Upon ligand binding, GPCRs undergo conformational changes that facilitate the binding and activation of multiple effectors. GPCRs regulate nearly all physiological processes and are a favorite pharmacological target. In particular, drugs are sought after that elicit the recruitment of selected effectors only (biased ligands). Understanding how ligands bind to GPCRs and which conformational changes they induce is a fundamental step toward the development of more efficient and specific drugs. Moreover, it is emerging that the dynamic of the ligand–receptor interaction contributes to the specificity of both ligand recognition and effector recruitment, an aspect that is missing in structural snapshots from crystallography. We describe here biochemical and biophysical techniques to address ligand–receptor interactions in their structural and dynamic aspects, which include mutagenesis, crosslinking, spectroscopic techniques, and mass-spectrometry profiling. With a main focus on peptide receptors, we present methods to unveil the ligand–receptor contact interface and methods that address conformational changes both in the ligand and the GPCR. The presented studies highlight a wide structural heterogeneity among peptide receptors, reveal distinct structural changes occurring during ligand binding and a surprisingly high dynamics of the ligand–GPCR complexes.
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13
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Zhu L, Bu G, Jing L, Shi D, Lee MY, Gonen T, Liu W, Nannenga BL. Structure Determination from Lipidic Cubic Phase Embedded Microcrystals by MicroED. Structure 2020; 28:1149-1159.e4. [PMID: 32735770 PMCID: PMC7544639 DOI: 10.1016/j.str.2020.07.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 06/02/2020] [Accepted: 07/13/2020] [Indexed: 01/22/2023]
Abstract
The lipidic cubic phase (LCP) technique has proved to facilitate the growth of high-quality crystals that are otherwise difficult to grow by other methods. However, the crystal size optimization process could be time and resource consuming, if it ever happens. Therefore, improved techniques for structure determination using these small crystals is an important strategy in diffraction technology development. Microcrystal electron diffraction (MicroED) is a technique that uses a cryo-transmission electron microscopy to collect electron diffraction data and determine high-resolution structures from very thin micro- and nanocrystals. In this work, we have used modified LCP and MicroED protocols to analyze crystals embedded in LCP converted by 2-methyl-2,4-pentanediol or lipase, including Proteinase K crystals grown in solution, cholesterol crystals, and human adenosine A2A receptor crystals grown in LCP. These results set the stage for the use of MicroED to analyze microcrystalline samples grown in LCP, especially for those highly challenging membrane protein targets.
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Affiliation(s)
- Lan Zhu
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA; School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA
| | - Guanhong Bu
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA; School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, USA
| | - Liang Jing
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA; School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA
| | - Dan Shi
- Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Ming-Yue Lee
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA; School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA
| | - Tamir Gonen
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Departments of Biological Chemistry and Physiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Wei Liu
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA; School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA.
| | - Brent L Nannenga
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA; School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, USA.
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Kögler LM, Stichel J, Beck-Sickinger AG. Structural investigations of cell-free expressed G protein-coupled receptors. Biol Chem 2020; 401:97-116. [PMID: 31539345 DOI: 10.1515/hsz-2019-0292] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 09/02/2019] [Indexed: 12/11/2022]
Abstract
G protein-coupled receptors (GPCRs) are of great pharmaceutical interest and about 35% of the commercial drugs target these proteins. Still there is huge potential left in finding molecules that target new GPCRs or that modulate GPCRs differentially. For a rational drug design, it is important to understand the structure, binding and activation of the protein of interest. Structural investigations of GPCRs remain challenging, although huge progress has been made in the last 20 years, especially in the generation of crystal structures of GPCRs. This is mostly caused by issues with the expression yield, purity or labeling. Cell-free protein synthesis (CFPS) is an efficient alternative for recombinant expression systems that can potentially address many of these problems. In this article the use of CFPS for structural investigations of GPCRs is reviewed. We compare different CFPS systems, including the cellular basis and reaction configurations, and strategies for an efficient solubilization. Next, we highlight recent advances in the structural investigation of cell-free expressed GPCRs, with special emphasis on the role of photo-crosslinking approaches to investigate ligand binding sites on GPCRs.
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Affiliation(s)
- Lisa Maria Kögler
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, Leipzig University, Brüderstr. 34, D-04103 Leipzig, Germany
| | - Jan Stichel
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, Leipzig University, Brüderstr. 34, D-04103 Leipzig, Germany
| | - Annette G Beck-Sickinger
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, Leipzig University, Brüderstr. 34, D-04103 Leipzig, Germany
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15
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The discovery of a new antibody for BRIL-fused GPCR structure determination. Sci Rep 2020; 10:11669. [PMID: 32669569 PMCID: PMC7363855 DOI: 10.1038/s41598-020-68355-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 06/21/2020] [Indexed: 12/17/2022] Open
Abstract
G-protein-coupled receptors (GPCRs)—the largest family of cell-surface membrane proteins—mediate the intracellular signal transduction of many external ligands. Thus, GPCRs have become important drug targets. X-ray crystal structures of GPCRs are very useful for structure-based drug design (SBDD). Herein, we produced a new antibody (SRP2070) targeting the thermostabilised apocytochrome b562 from Escherichia coli M7W/H102I/R106L (BRIL). We found that a fragment of this antibody (SRP2070Fab) facilitated the crystallisation of the BRIL-tagged, ligand bound GPCRs, 5HT1B and AT2R. Furthermore, the electron densities of the ligands were resolved, suggesting that SPR2070Fab is versatile and adaptable for GPCR SBDD. We anticipate that this new tool will significantly accelerate structure determination of other GPCRs and the design of small molecular drugs targeting them.
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16
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Tumor-induced neurogenesis and immune evasion as targets of innovative anti-cancer therapies. Signal Transduct Target Ther 2020; 5:99. [PMID: 32555170 PMCID: PMC7303203 DOI: 10.1038/s41392-020-0205-z] [Citation(s) in RCA: 115] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 05/15/2020] [Accepted: 05/24/2020] [Indexed: 12/11/2022] Open
Abstract
Normal cells are hijacked by cancer cells forming together heterogeneous tumor masses immersed in aberrant communication circuits that facilitate tumor growth and dissemination. Besides the well characterized angiogenic effect of some tumor-derived factors; others, such as BDNF, recruit peripheral nerves and leukocytes. The neurogenic switch, activated by tumor-derived neurotrophins and extracellular vesicles, attracts adjacent peripheral fibers (autonomic/sensorial) and neural progenitor cells. Strikingly, tumor-associated nerve fibers can guide cancer cell dissemination. Moreover, IL-1β, CCL2, PGE2, among other chemotactic factors, attract natural immunosuppressive cells, including T regulatory (Tregs), myeloid-derived suppressor cells (MDSCs), and M2 macrophages, to the tumor microenvironment. These leukocytes further exacerbate the aberrant communication circuit releasing factors with neurogenic effect. Furthermore, cancer cells directly evade immune surveillance and the antitumoral actions of natural killer cells by activating immunosuppressive mechanisms elicited by heterophilic complexes, joining cancer and immune cells, formed by PD-L1/PD1 and CD80/CTLA-4 plasma membrane proteins. Altogether, nervous and immune cells, together with fibroblasts, endothelial, and bone-marrow-derived cells, promote tumor growth and enhance the metastatic properties of cancer cells. Inspired by the demonstrated, but restricted, power of anti-angiogenic and immune cell-based therapies, preclinical studies are focusing on strategies aimed to inhibit tumor-induced neurogenesis. Here we discuss the potential of anti-neurogenesis and, considering the interplay between nervous and immune systems, we also focus on anti-immunosuppression-based therapies. Small molecules, antibodies and immune cells are being considered as therapeutic agents, aimed to prevent cancer cell communication with neurons and leukocytes, targeting chemotactic and neurotransmitter signaling pathways linked to perineural invasion and metastasis.
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Yang J, Gong Z, Lu YB, Xu CJ, Wei TF, Yang MS, Zhan TW, Yang YH, Lin L, Liu J, Tang C, Zhang WP. FLIM-FRET-Based Structural Characterization of a Class-A GPCR Dimer in the Cell Membrane. J Mol Biol 2020; 432:4596-4611. [PMID: 32553728 DOI: 10.1016/j.jmb.2020.06.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 06/10/2020] [Accepted: 06/10/2020] [Indexed: 12/30/2022]
Abstract
Class-A G protein-coupled receptors (GPCRs) are known to homo-dimerize in the membrane. Yet, methods to characterize the structure of GPCR dimer in the native environment are lacking. Accordingly, the molecular basis and functional relevance of the class-A GPCR dimerization remain unclear. Here, we present the dimeric structural model of GPR17 in the cell membrane. The dimer mainly involves transmembrane helix 5 (TM5) at the interface, with F229 in TM5, a critical residue. An F229A mutation makes GPR17 monomeric regardless of the expression level of the receptor. Monomeric mutants of GPR17 display impaired ERK1/2 activation and cannot be properly internalized upon agonist treatment. Conversely, the F229C mutant is cross-linked as a dimer and behaves like wild-type. Importantly, the GPR17 dimer structure has been modeled using sparse inter-protomer FRET distance restraints obtained from fluorescence lifetime imaging microscopy. The same approach can be applied to characterizing the interactions of other important membrane proteins in the cell.
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Affiliation(s)
- Ju Yang
- Key Laboratory of Magnetic Resonance in Biological Systems of the Chinese Academy of Sciences, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy of Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhou Gong
- Key Laboratory of Magnetic Resonance in Biological Systems of the Chinese Academy of Sciences, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy of Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Yun-Bi Lu
- Department of Pharmacology and Department Of Neurosurgery, Key Laboratory of Medical Neurobiology of Ministry of Health of China, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Chan-Juan Xu
- College of Life Science and Technology, International Research Center for Sensory Biology and Technology of MOST, Key Laboratory of Molecular Biophysics of Ministry of Education, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Tao-Feng Wei
- Department of Pharmacology and Department Of Neurosurgery, Key Laboratory of Medical Neurobiology of Ministry of Health of China, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Meng-Shi Yang
- Key Laboratory of Magnetic Resonance in Biological Systems of the Chinese Academy of Sciences, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy of Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Tian-Wei Zhan
- Department of Thoracic Surgery, the Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang 310009, China
| | - Yu-Hong Yang
- Key Laboratory of Magnetic Resonance in Biological Systems of the Chinese Academy of Sciences, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy of Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Li Lin
- College of Life Science and Technology, International Research Center for Sensory Biology and Technology of MOST, Key Laboratory of Molecular Biophysics of Ministry of Education, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Jianfeng Liu
- College of Life Science and Technology, International Research Center for Sensory Biology and Technology of MOST, Key Laboratory of Molecular Biophysics of Ministry of Education, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.
| | - Chun Tang
- Key Laboratory of Magnetic Resonance in Biological Systems of the Chinese Academy of Sciences, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy of Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China; Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei Province 430074, China.
| | - Wei-Ping Zhang
- Department of Pharmacology and Department Of Neurosurgery, Key Laboratory of Medical Neurobiology of Ministry of Health of China, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.
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18
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Insights into adenosine A2A receptor activation through cooperative modulation of agonist and allosteric lipid interactions. PLoS Comput Biol 2020; 16:e1007818. [PMID: 32298258 PMCID: PMC7188303 DOI: 10.1371/journal.pcbi.1007818] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 04/28/2020] [Accepted: 03/23/2020] [Indexed: 12/18/2022] Open
Abstract
The activation process of G protein-coupled receptors (GPCRs) has been extensively studied, both experimentally and computationally. In particular, Molecular Dynamics (MD) simulations have proven useful in exploring GPCR conformational space. The typical behaviour of class A GPCRs, when subjected to unbiased MD simulations from their crystallized inactive state, is to fluctuate between inactive and intermediate(s) conformations, even with bound agonist. Fully active conformation(s) are rarely stabilized unless a G protein is also bound. Despite several crystal structures of the adenosine A2a receptor (A2aR) having been resolved in complex with co-crystallized agonists and Gs protein, its agonist-mediated activation process is still not completely understood. In order to thoroughly examine the conformational landscape of A2aR activation, we performed unbiased microsecond-length MD simulations in quadruplicate, starting from the inactive conformation either in apo or with bound agonists: endogenous adenosine or synthetic NECA, embedded in two homogeneous phospholipid membranes: 1,2-dioleoyl-sn-glycerol-3-phosphoglycerol (DOPG) or 1,2-dioleoyl-sn-glycerol-3-phosphocholine (DOPC). In DOPC with bound adenosine or NECA, we observe transition to an intermediate receptor conformation consistent with the known adenosine-bound crystal state. In apo state in DOPG, two different intermediate conformations are obtained. One is similar to that observed with bound adenosine in DOPC, while the other is closer to the active state but not yet fully active. Exclusively, in DOPG with bound adenosine or NECA, we reproducibly identify receptor conformations with fully active features, which are able to dock Gs protein. These different receptor conformations can be attributed to the action/absence of agonist and phospholipid-mediated allosteric effects on the intracellular side of the receptor.
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19
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Evaluating the benefits of renin-angiotensin system inhibitors as cancer treatments. Pharmacol Ther 2020; 211:107527. [PMID: 32173557 DOI: 10.1016/j.pharmthera.2020.107527] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 03/08/2020] [Indexed: 02/07/2023]
Abstract
G-protein-coupled receptors (GPCRs) are the largest and most diverse group of cellular membrane receptors identified and characterized. It is estimated that 30 to 50% of marketed drugs target these receptors. The angiotensin II receptor type 1 (AT1R) is a GPCR which signals in response to systemic alterations of the peptide hormone angiotensin II (AngII) in circulation. The enzyme responsible for converting AngI to AngII is the angiotensin-converting enzyme (ACE). Specific inhibitors for the AT1R (more commonly known as AT1R blockers or antagonists) and ACE are well characterized for their effects on the cardiovascular system. Combined with the extensive clinical data available on patient tolerance of AT1R blockers (ARBs) and ACE inhibitors (ACEIs), as well as their non-classical roles in cancer, the notion of repurposing this class of medications as cancer treatment(s) is explored in the current review. Given that AngII-dependent AT1R activity directly regulates angiogenesis, remodeling of vasculature, pro-inflammatory responses, stem cell programming and hematopoiesis, and electrolyte balance; the modulation of these processes with pharmacologically well characterized medications could present a valuable complementary treatment option for cancer patients.
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20
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Structural equilibrium underlying ligand-dependent activation of β2-adrenoreceptor. Nat Chem Biol 2020; 16:430-439. [DOI: 10.1038/s41589-019-0457-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 12/01/2019] [Accepted: 12/17/2019] [Indexed: 11/08/2022]
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21
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Miljus T, Sykes DA, Harwood CR, Vuckovic Z, Veprintsev DB. GPCR Solubilization and Quality Control. Methods Mol Biol 2020; 2127:105-127. [PMID: 32112318 DOI: 10.1007/978-1-0716-0373-4_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
G protein-coupled receptors (GPCRs) are versatile membrane proteins involved in the regulation of many physiological processes and pathological conditions, making them interesting pharmacological targets. In order to study their structure and function, GPCRs are traditionally extracted from membranes using detergents. However, due to their hydrophobic nature, intrinsic instability in aqueous solutions, and their denaturing effects, the isolation of properly folded and functional GPCRs is not trivial. Therefore, it is of crucial importance to solubilize receptors under mild conditions and control the sample quality subsequently. Here we describe widely used methods for small-scale GPCR solubilization, followed by quality control based on fluorescence size-exclusion chromatography, SDS-PAGE, temperature-induced protein unfolding (CPM dye binding) and fluorescent ligand binding assay. These methods can easily be used to assess the thermostability and functionality of a GPCR sample exposed to different conditions, such as the use of various detergents, addition of lipids and ligands, making them valuable for obtaining an optimal sample quality for structural and functional studies.
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Affiliation(s)
- Tamara Miljus
- Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
- Department of Biology, ETH Zürich, Zürich, Switzerland
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - David A Sykes
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Clare R Harwood
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Ziva Vuckovic
- Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
- Department of Biology, ETH Zürich, Zürich, Switzerland
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Dmitry B Veprintsev
- Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland.
- Department of Biology, ETH Zürich, Zürich, Switzerland.
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK.
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, UK.
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22
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Small-scale approach for precrystallization screening in GPCR X-ray crystallography. Nat Protoc 2019; 15:144-160. [PMID: 31784719 DOI: 10.1038/s41596-019-0259-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 10/28/2019] [Indexed: 12/25/2022]
Abstract
G protein-coupled receptors (GPCRs) are important pharmaceutical targets. Knowledge of their 3D structures is critical to understanding mechanisms of drug action. Low cellular expression, purification yield, and in vitro instability are substantial hurdles to the successful determination of GPCR structure. Intense effort is required to optimize a receptor's protein sequence and purification procedure, increasing the complexity of the precrystallization process. Here, we present a procedure for a small-scale precrystallization screen that involves detecting GPCR expression levels in Spodoptera frugiperda (Sf9) culture by flow cytometry and evaluating GPCR stability by size-exclusion chromatography and UV absorbance measurements. The example procedure uses the smallest volumes of Sf9 cell culture that will yield sufficient quantities of purified protein for intrinsic UV absorbance analysis and is amenable to medium throughput with the same constructs and conditions that would be scaled up for crystallization trials. The protocol takes 8 d to complete and requires expertise in cell culture, protein purification, and chromatography.
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Ishchenko A, Stauch B, Han GW, Batyuk A, Shiriaeva A, Li C, Zatsepin N, Weierstall U, Liu W, Nango E, Nakane T, Tanaka R, Tono K, Joti Y, Iwata S, Moraes I, Gati C, Cherezov V. Toward G protein-coupled receptor structure-based drug design using X-ray lasers. IUCRJ 2019; 6:1106-1119. [PMID: 31709066 PMCID: PMC6830214 DOI: 10.1107/s2052252519013137] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 09/23/2019] [Indexed: 06/10/2023]
Abstract
Rational structure-based drug design (SBDD) relies on the availability of a large number of co-crystal structures to map the ligand-binding pocket of the target protein and use this information for lead-compound optimization via an iterative process. While SBDD has proven successful for many drug-discovery projects, its application to G protein-coupled receptors (GPCRs) has been limited owing to extreme difficulties with their crystallization. Here, a method is presented for the rapid determination of multiple co-crystal structures for a target GPCR in complex with various ligands, taking advantage of the serial femtosecond crystallography approach, which obviates the need for large crystals and requires only submilligram quantities of purified protein. The method was applied to the human β2-adrenergic receptor, resulting in eight room-temperature co-crystal structures with six different ligands, including previously unreported structures with carvedilol and propranolol. The generality of the proposed method was tested with three other receptors. This approach has the potential to enable SBDD for GPCRs and other difficult-to-crystallize membrane proteins.
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Affiliation(s)
- Andrii Ishchenko
- Bridge Institute, Departments of Chemistry and Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Benjamin Stauch
- Bridge Institute, Departments of Chemistry and Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Gye Won Han
- Bridge Institute, Departments of Chemistry and Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Alexander Batyuk
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Anna Shiriaeva
- Bridge Institute, Departments of Chemistry and Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Chufeng Li
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Nadia Zatsepin
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Uwe Weierstall
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Wei Liu
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Eriko Nango
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Takanori Nakane
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo, Tokyo 113-0032, Japan
| | - Rie Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Yasumasa Joti
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - So Iwata
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Isabel Moraes
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, England
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0FA, England
| | - Cornelius Gati
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
- Biosciences Division, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Vadim Cherezov
- Bridge Institute, Departments of Chemistry and Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
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24
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Solid-State NMR Approaches to Study Protein Structure and Protein-Lipid Interactions. Methods Mol Biol 2019. [PMID: 31218633 DOI: 10.1007/978-1-4939-9512-7_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Solid-state NMR spectroscopy has been developed for the investigation of membrane-associated polypeptides and remains one of the few techniques to reveal high-resolution structural information in liquid-disordered phospholipid bilayers. In particular, oriented samples have been used to investigate the structure, dynamics and topology of membrane polypeptides. Much of the previous solid-state NMR work has been developed and performed on peptides but the technique is constantly expanding towards larger membrane proteins. Here, a number of protocols are presented describing among other the reconstitution of membrane proteins into oriented membranes, monitoring membrane alignment by 31P solid-state NMR spectroscopy, investigations of the protein by one- and two-dimensional 15N solid-state NMR and measurements of the lipid order parameters using 2H solid-state NMR spectroscopy. Using such methods solid-state NMR spectroscopy has revealed a detailed picture of the ensemble of both lipids and proteins and their mutual interdependence in the bilayer environment.
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Mahmod Al-Qattan MN, Mordi MN. Molecular Basis of Modulating Adenosine Receptors Activities. Curr Pharm Des 2019; 25:817-831. [DOI: 10.2174/1381612825666190304122624] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 02/26/2019] [Indexed: 01/04/2023]
Abstract
Modulating cellular processes through extracellular chemical stimuli is medicinally an attractive approach to control disease conditions. GPCRs are the most important group of transmembranal receptors that produce different patterns of activations using intracellular mediators (such as G-proteins and Beta-arrestins). Adenosine receptors (ARs) belong to GPCR class and are divided into A1AR, A2AAR, A2BAR and A3AR. ARs control different physiological activities thus considered valuable target to control neural, heart, inflammatory and other metabolic disorders. Targeting ARs using small molecules essentially works by binding orthosteric and/or allosteric sites of the receptors. Although targeting orthosteric site is considered typical to modulate receptor activity, allosteric sites provide better subtype selectivity, saturable modulation of activity and variable activation patterns. Each receptor exists in dynamical equilibrium between conformational ensembles. The equilibrium is affected by receptor interaction with other molecules. Changing the population of conformational ensembles of the receptor is the method by which orthosteric, allosteric and other cellular components control receptor signaling. Herein, the interactions of ARs with orthosteric, allosteric ligands as well as intracellular mediators are described. A quinary interaction model for the receptor is proposed and energy wells for major conformational ensembles are retrieved.
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Affiliation(s)
| | - Mohd Nizam Mordi
- Centre For Drug Research, Universiti Sains Malaysia, 11800 Gelugor, Penang, Malaysia
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26
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Itoigawa A, Hayakawa T, Suzuki-Hashido N, Imai H. A natural point mutation in the bitter taste receptor TAS2R16 causes inverse agonism of arbutin in lemur gustation. Proc Biol Sci 2019; 286:20190884. [PMID: 31161904 DOI: 10.1098/rspb.2019.0884] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Bitter taste enables the detection of potentially harmful substances and is mediated by bitter taste receptors, TAS2Rs, in vertebrates. Few antagonists and inverse agonists of TAS2Rs have been identified, especially natural compounds. TAS2R16s in humans, apes and Old World monkeys (Catarrhini, Anthropoidea) recognize β-glucoside analogues as specific agonists. Here, we investigated responses of TAS2R16 to β-glucosides in non-anthropoid primates, namely lemurs (Lemuriformes, Strepsirrhini). Salicin acted as an agonist on lemur TAS2R16. Arbutin acted as an agonist in the ring-tailed lemur ( Lemur catta) but as an inverse agonist in black lemur ( Eulemur macaco) and black-and-white ruffed lemur ( Varecia variegata). We identified a strepsirrhine-specific amino acid substitution responsible for the inverse agonism of arbutin. In a food preference test, salicin bitterness was inhibited by arbutin in the black lemur. Structural modelling revealed this locus was important for a rearrangement of the intracellular end of transmembrane helix 7 (TM7). Accordingly, arbutin is the first known natural inverse agonist of TAS2Rs, contributing to our understanding of receptor-ligand interactions and the molecular basis of the unique feeding habit diversification in lemurs. Furthermore, the identification of a causal point mutation suggests that TAS2R can acquire functional changes according to feeding habits and environmental conditions.
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Affiliation(s)
- Akihiro Itoigawa
- 1 Molecular Biology Section, Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University , 41-2 Kanrin, Inuyama, Aichi 484-8506 , Japan.,3 Japan Society for the Promotion of Science , Kojimachi, Chiyoda-ku, Tokyo 102-0083 , Japan
| | - Takashi Hayakawa
- 2 Department of Wildlife Science (Nagoya Railroad Co., Ltd.), Primate Research Institute, Kyoto University , 41-2 Kanrin, Inuyama, Aichi 484-8506 , Japan.,4 Faculty of Environmental Earth Science, Hokkaido University , N10W5, Kita-ku, Sapporo, Hokkaido 060-0810 , Japan.,5 Japan Monkey Centre , 26 Inuyamakanrin, Inuyama, Aichi 484-0081 , Japan
| | - Nami Suzuki-Hashido
- 3 Japan Society for the Promotion of Science , Kojimachi, Chiyoda-ku, Tokyo 102-0083 , Japan.,6 Chubu University Academy of Emerging Sciences , 1200 Matsumoto-cho, Kasugai, Aichi 487-8501 , Japan
| | - Hiroo Imai
- 1 Molecular Biology Section, Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University , 41-2 Kanrin, Inuyama, Aichi 484-8506 , Japan
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27
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Syed Haneef SA, Ranganathan S. Structural bioinformatics analysis of variants on GPCR function. Curr Opin Struct Biol 2019; 55:161-177. [PMID: 31174013 DOI: 10.1016/j.sbi.2019.04.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/20/2019] [Accepted: 04/22/2019] [Indexed: 10/26/2022]
Abstract
G protein-coupled receptors (GPCRs) are key membrane-embedded receptor proteins, with critical roles in cellular signal transduction. In the era of precision medicine, understanding the role of natural variants on GPCR function is critical, especially from a pharmacogenomics viewpoint. Studies involved in mapping variants to GPCR structures are briefly reviewed here. The endocannabinoid system involving the central nervous system (CNS), the human cannabinoid receptor 1 (CB1), is an important drug target and its variability has implications for disease susceptibility and altered drug and pain response. We have carried out a computational study to map deleterious non-synonymous single nucleotide polymorphisms (nsSNPs) to CB1. CB1 mutations were computationally evaluated from neutral to deleterious, and the top twelve deleterious mutations, with structural information, were found to be either close to the ligand binding region or the G-protein binding site. We have mapped these to the active and inactive CB1 X-ray crystallographic structures to correlate variants with available phenotypic information. We have also carried out molecular dynamics simulations to functionally characterize four selected mutants.
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Affiliation(s)
- Syed Askar Syed Haneef
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, NSW 2109, Australia
| | - Shoba Ranganathan
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, NSW 2109, Australia.
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28
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Chen M, Jing Y, Wang L, Feng Z, Xie XQ. DAKB-GPCRs: An Integrated Computational Platform for Drug Abuse Related GPCRs. J Chem Inf Model 2019; 59:1283-1289. [PMID: 30835466 PMCID: PMC6758544 DOI: 10.1021/acs.jcim.8b00623] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Drug abuse (DA) or drug addiction is a complicated brain disorder which is commonly considered as neurobiological impairments caused by both genetic factors and environmental effects. Among DA-related targets, G protein-coupled receptors (GPCRs) play an important role in DA therapy. However, only 52 GPCRs have been published with crystal structures in the recent two decades. In the effort to overcome the limitations of crystal structure and conformational diversity of GPCRs, we built homology models and performed conformational searches by molecular dynamics (MD) simulation. To accelerate and facilitate the drug abuse research, we construct a DA-related GPCR-specific chemogenomics knowledgebase (KB) (DAKB-GPCRs) for its research that can be implemented with our established and novel chemogenomics tools as well as algorithms for data analysis and visualization. Our established TargetHunter and HTDocking tools, as well as our novel tools that include target classification and Spider Plot, are compiled into the platform. Our DAKB-GPCRs provides the following results for a query compound: (1) blood-brain barrier (BBB) plot via our BBB predictor, (2) docking scores via HTDocking, (3) similarity score via TargetHunter, (4) target classification via machine learning methods that utilize both docking scores and similarity scores, and (5) a drug-target interaction network via Spider Plot.
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Affiliation(s)
- Maozi Chen
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, Pittsburgh, Pennsylvania 15261, United States
- NIH National Center of Excellence for Computational Drug Abuse Research, Pittsburgh, Pennsylvania 15261, United States
- Drug Discovery Institute, Pittsburgh, Pennsylvania 15261, United States
| | - Yankang Jing
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, Pittsburgh, Pennsylvania 15261, United States
- NIH National Center of Excellence for Computational Drug Abuse Research, Pittsburgh, Pennsylvania 15261, United States
- Drug Discovery Institute, Pittsburgh, Pennsylvania 15261, United States
| | - Lirong Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, Pittsburgh, Pennsylvania 15261, United States
- NIH National Center of Excellence for Computational Drug Abuse Research, Pittsburgh, Pennsylvania 15261, United States
- Drug Discovery Institute, Pittsburgh, Pennsylvania 15261, United States
| | - Zhiwei Feng
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, Pittsburgh, Pennsylvania 15261, United States
- NIH National Center of Excellence for Computational Drug Abuse Research, Pittsburgh, Pennsylvania 15261, United States
- Drug Discovery Institute, Pittsburgh, Pennsylvania 15261, United States
| | - Xiang-Qun Xie
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, Pittsburgh, Pennsylvania 15261, United States
- NIH National Center of Excellence for Computational Drug Abuse Research, Pittsburgh, Pennsylvania 15261, United States
- Drug Discovery Institute, Pittsburgh, Pennsylvania 15261, United States
- Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
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29
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Computer aided protein engineering to enhance the thermo-stability of CXCR1- T4 lysozyme complex. Sci Rep 2019; 9:5317. [PMID: 30926935 PMCID: PMC6441008 DOI: 10.1038/s41598-019-41838-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 03/19/2019] [Indexed: 01/01/2023] Open
Abstract
CXCR1, a member in G-protein coupled receptor (GPCR) family, binds to chemokine interleukin-8 (IL-8) specifically and transduces signals to mediate immune and inflammatory responses. Despite the importance of CXCR1, high-resolution structure determination is hindered by the challenges in crystallization. It has been shown that properly designed mutants with enhanced thermostability, together with fusion partner proteins, can be useful to form crystals for GPCR proteins. In this study, in silico protein design was carried out by using homology modeling and molecular dynamics simulations. To validate the computational modeling results, the thermostability of several mutants and the wild type were measured experimentally. Both computational results and experimental data suggest that the mutant L126W has a significant improvement in the thermostability. This study demonstrated that in silico design can guide protein engineering and potentially facilitate protein crystallography research.
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30
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Kögler LM, Stichel J, Kaiser A, Beck-Sickinger AG. Cell-Free Expression and Photo-Crosslinking of the Human Neuropeptide Y 2 Receptor. Front Pharmacol 2019; 10:176. [PMID: 30881304 PMCID: PMC6405639 DOI: 10.3389/fphar.2019.00176] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 02/11/2019] [Indexed: 12/15/2022] Open
Abstract
G protein-coupled receptors (GPCRs) represent a large family of different proteins, which are involved in physiological processes throughout the entire body. Furthermore, they represent important drug targets. For rational drug design, it is important to get further insights into the binding mode of endogenous ligands as well as of therapeutic agents at the respective target receptors. However, structural investigations usually require homogenous, solubilized and functional receptors, which is still challenging. Cell-free expression methods have emerged in the last years and many different proteins are successfully expressed, including hydrophobic membrane proteins like GPCRs. In this work, an Escherichia coli based cell-free expression system was used to express the neuropeptide Y2 receptor (Y2R) for structural investigations. This GPCR was expressed in two different variants, a C-terminal enhanced green fluorescent fusion protein and a cysteine deficient variant. In order to obtain soluble receptors, the expression was performed in the presence of mild detergents, either Brij-35 or Brij-58, which led to high amounts of soluble receptor. Furthermore, the influence of temperature, pH value and additives on protein expression and solubilization was tested. For functional and structural investigations, the receptors were expressed at 37°C, pH 7.4 in the presence of 1 mM oxidized and 5 mM reduced glutathione. The expressed receptors were purified by ligand affinity chromatography and functionality of Y2R_cysteine_deficient was verified by a homogenous binding assay. Finally, photo-crosslinking studies were performed between cell-free expressed Y2R_cysteine_deficient and a neuropeptide Y (NPY) analog bearing the photoactive, unnatural amino acid p-benzoyl-phenylalanine at position 27 and biotin at position 22 for purification. After enzymatic digestion, fragments of crosslinked receptor were identified by mass spectrometry. Our findings demonstrate that, in contrast to Y1R, NPY position 27 remains flexible when bound to Y2R. These results are in agreement with the suggested binding mode of NPY at Y2R.
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Affiliation(s)
- Lisa Maria Kögler
- Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, Leipzig, Germany
| | - Jan Stichel
- Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, Leipzig, Germany
| | - Anette Kaiser
- Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, Leipzig, Germany
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31
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Abstract
Innovations are expanding the capabilities of experimental investigations of the structural properties of membrane proteins. Traditionally, three-dimensional structures have been determined by measuring x-ray diffraction using protein crystals with a size of least 100 μm. For membrane proteins, achieving crystals suitable for these measurements has been a significant challenge. The availabilities of micro-focus x-ray beams and the new instrumentation of x-ray free-electron lasers have opened up the possibility of using submicrometer-sized crystals. In addition, advances in cryo-electron microscopy have expanded the use of this technique for studies of protein crystals as well as studies of individual proteins as single particles. Together, these approaches provide unprecedented opportunities for the exploration of structural properties of membrane proteins, including dynamical changes during protein function.
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Affiliation(s)
- James P Allen
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
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32
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Audet M, Stevens RC. Emerging structural biology of lipid G protein-coupled receptors. Protein Sci 2019; 28:292-304. [PMID: 30239054 PMCID: PMC6319753 DOI: 10.1002/pro.3509] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 09/07/2018] [Accepted: 09/10/2018] [Indexed: 01/14/2023]
Abstract
The first crystal structure of a G protein-coupled receptor (GPCR) was that of the bovine rhodopsin, solved in 2000, and is a light receptor within retina rode cells that enables vision by transducing a conformational signal from the light-induced isomerization of retinal covalently bound to the receptor. More than 7 years after this initial discovery and following more than 20 years of technological developments in GPCR expression, stabilization, and crystallography, the high-resolution structure of the adrenaline binding β2 -adrenergic receptor, a ligand diffusible receptor, was discovered. Since then, high-resolution structures of more than 53 unique GPCRs have been determined leading to a significant improvement in our understanding of the basic mechanisms of ligand-binding and ligand-mediated receptor activation that revolutionized the field of structural molecular pharmacology of GPCRs. Recently, several structures of eight unique lipid-binding receptors, one of the most difficult GPCR families to study, have been reported. This review presents the outstanding structural and pharmacological features that have emerged from these new lipid receptor structures. The impact of these findings goes beyond mechanistic insights, providing evidence of the fundamental role of GPCRs in the physiological integration of the lipid signaling system, and highlighting the importance of sustained research into the structural biology of GPCRs for the development of new therapeutics targeting lipid receptors.
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Affiliation(s)
- Martin Audet
- Departments of Biological Sciences and ChemistryBridge Institute, Michelson Center for Convergent Bioscience, University of Southern CaliforniaLos AngelesCalifornia90089
| | - Raymond C. Stevens
- Departments of Biological Sciences and ChemistryBridge Institute, Michelson Center for Convergent Bioscience, University of Southern CaliforniaLos AngelesCalifornia90089
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33
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Ye N, Li B, Mao Q, Wold EA, Tian S, Allen JA, Zhou J. Orphan Receptor GPR88 as an Emerging Neurotherapeutic Target. ACS Chem Neurosci 2019; 10:190-200. [PMID: 30540906 DOI: 10.1021/acschemneuro.8b00572] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Although G protein-coupled receptors (GPCRs) are recognized as pivotal drug targets involved in multiple physiological and pathological processes, the majority of GPCRs including orphan GPCRs (oGPCRs) are unexploited. GPR88, a brain-specific oGPCR with particularly robust expression in the striatum, regulates diverse brain and behavioral functions, including cognition, mood, movement control, and reward-based learning, and is thus emerging as a novel drug target for central nervous system disorders including schizophrenia, Parkinson's disease, anxiety, and addiction. Nevertheless, no effective GPR88 synthetic ligands have yet entered into clinical trials, and GPR88 endogenous ligands remain unknown. Despite the recent discovery and early stage study of several GPR88 agonists, such as 2-PCCA, RTI-13951-33, and phenylglycinol derivatives, further research into GPR88 pharmacology, medicinal chemistry, and chemical biology is urgently needed to yield structurally diversified GPR88-specific ligands. Drug-like pharmacological tool function and relevant signaling elucidation will also accelerate the evaluation of this receptor as a viable neurotherapeutic target.
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Affiliation(s)
- Na Ye
- Department of Medicinal Chemistry, Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
- Department of Pharmacology and Toxicology, Center for Addiction Research, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Bang Li
- Department of Medicinal Chemistry, Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Qi Mao
- Department of Medicinal Chemistry, Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Eric A. Wold
- Department of Pharmacology and Toxicology, Center for Addiction Research, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Sheng Tian
- Department of Medicinal Chemistry, Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - John A. Allen
- Department of Pharmacology and Toxicology, Center for Addiction Research, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Jia Zhou
- Department of Pharmacology and Toxicology, Center for Addiction Research, University of Texas Medical Branch, Galveston, Texas 77555, United States
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34
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Audet M, White KL, Breton B, Zarzycka B, Han GW, Lu Y, Gati C, Batyuk A, Popov P, Velasquez J, Manahan D, Hu H, Weierstall U, Liu W, Shui W, Katritch V, Cherezov V, Hanson MA, Stevens RC. Crystal structure of misoprostol bound to the labor inducer prostaglandin E 2 receptor. Nat Chem Biol 2019; 15:11-17. [PMID: 30510194 PMCID: PMC6289721 DOI: 10.1038/s41589-018-0160-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 09/05/2018] [Indexed: 01/07/2023]
Abstract
Misoprostol is a life-saving drug in many developing countries for women at risk of post-partum hemorrhaging owing to its affordability, stability, ease of administration and clinical efficacy. However, misoprostol lacks receptor and tissue selectivities, and thus its use is accompanied by a number of serious side effects. The development of pharmacological agents combining the advantages of misoprostol with improved selectivity is hindered by the absence of atomic details of misoprostol action in labor induction. Here, we present the 2.5 Å resolution crystal structure of misoprostol free-acid form bound to the myometrium labor-inducing prostaglandin E2 receptor 3 (EP3). The active state structure reveals a completely enclosed binding pocket containing a structured water molecule that coordinates misoprostol's ring structure. Modeling of selective agonists in the EP3 structure reveals rationales for selectivity. These findings will provide the basis for the next generation of uterotonic drugs that will be suitable for administration in low resource settings.
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Affiliation(s)
- Martin Audet
- Departments of Biological Sciences and Chemistry, Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
| | - Kate L. White
- Departments of Biological Sciences and Chemistry, Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
| | - Billy Breton
- Domain Therapeutics NA Inc., Frederick-Banting Road, Montreal H4S 1Z9, Canada
| | - Barbara Zarzycka
- Departments of Biological Sciences and Chemistry, Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
| | - Gye Won Han
- Departments of Biological Sciences and Chemistry, Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
| | - Yan Lu
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Cornelius Gati
- Linac Coherent Light Source, SLAC, National Accelerator Laboratory, Menlo Park, California 94025, USA,Stanford University, Department of Structural Biology, Palo Alto, California 94305, USA
| | - Alexander Batyuk
- Linac Coherent Light Source, SLAC, National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Petr Popov
- Departments of Biological Sciences and Chemistry, Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA,Moscow Institute of Physics and Technology, Dolgoprudny, 141700, Russia
| | - Jeffrey Velasquez
- Departments of Biological Sciences and Chemistry, Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
| | - David Manahan
- Departments of Biological Sciences and Chemistry, Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
| | - Hao Hu
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, USA
| | - Uwe Weierstall
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, USA
| | - Wei Liu
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, USA
| | - Wenqing Shui
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Vsevolod Katritch
- Departments of Biological Sciences and Chemistry, Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA,Moscow Institute of Physics and Technology, Dolgoprudny, 141700, Russia
| | - Vadim Cherezov
- Departments of Biological Sciences and Chemistry, Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA,Moscow Institute of Physics and Technology, Dolgoprudny, 141700, Russia
| | | | - Raymond C. Stevens
- Departments of Biological Sciences and Chemistry, Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA,Correspondence:
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35
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Wu Z, Li W, Liu G, Tang Y. Network-Based Methods for Prediction of Drug-Target Interactions. Front Pharmacol 2018; 9:1134. [PMID: 30356768 PMCID: PMC6189482 DOI: 10.3389/fphar.2018.01134] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Accepted: 09/18/2018] [Indexed: 01/10/2023] Open
Abstract
Drug-target interaction (DTI) is the basis of drug discovery. However, it is time-consuming and costly to determine DTIs experimentally. Over the past decade, various computational methods were proposed to predict potential DTIs with high efficiency and low costs. These methods can be roughly divided into several categories, such as molecular docking-based, pharmacophore-based, similarity-based, machine learning-based, and network-based methods. Among them, network-based methods, which do not rely on three-dimensional structures of targets and negative samples, have shown great advantages over the others. In this article, we focused on network-based methods for DTI prediction, in particular our network-based inference (NBI) methods that were derived from recommendation algorithms. We first introduced the methodologies and evaluation of network-based methods, and then the emphasis was put on their applications in a wide range of fields, including target prediction and elucidation of molecular mechanisms of therapeutic effects or safety problems. Finally, limitations and perspectives of network-based methods were discussed. In a word, network-based methods provide alternative tools for studies in drug repurposing, new drug discovery, systems pharmacology and systems toxicology.
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Affiliation(s)
| | | | | | - Yun Tang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
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36
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Abstract
G protein-coupled receptors (GPCRs) represent a large superfamily of membrane proteins that mediate cell signaling and regulate a variety of physiological processes in the human body. Structure-function studies of this superfamily were enabled a decade ago by multiple breakthroughs in technology that included receptor stabilization, crystallization in a membrane environment, and microcrystallography. The recent emergence of X-ray free-electron lasers (XFELs) has further accelerated structural studies of GPCRs and other challenging proteins by overcoming radiation damage and providing access to high-resolution structures and dynamics using micrometer-sized crystals. Here, we summarize key technology advancements and major milestones of GPCR research using XFELs and provide a brief outlook on future developments in the field.
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Affiliation(s)
- Benjamin Stauch
- Department of Chemistry and Bridge Institute, University of Southern California, Los Angeles, California 90089, USA; ,
| | - Vadim Cherezov
- Department of Chemistry and Bridge Institute, University of Southern California, Los Angeles, California 90089, USA; ,
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37
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Lu S, Zhang J. Small Molecule Allosteric Modulators of G-Protein-Coupled Receptors: Drug–Target Interactions. J Med Chem 2018; 62:24-45. [DOI: 10.1021/acs.jmedchem.7b01844] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Shaoyong Lu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China
| | - Jian Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China
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38
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The G protein-coupled receptors deorphanization landscape. Biochem Pharmacol 2018; 153:62-74. [PMID: 29454621 DOI: 10.1016/j.bcp.2018.02.016] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 02/13/2018] [Indexed: 12/14/2022]
Abstract
G protein-coupled receptors (GPCRs) are usually highlighted as being both the largest family of membrane proteins and the most productive source of drug targets. However, most of the GPCRs are understudied and hence cannot be used immediately for innovative therapeutic strategies. Besides, there are still around 100 orphan receptors, with no described endogenous ligand and no clearly defined function. The race to discover new ligands for these elusive receptors seems to be less intense than before. Here, we present an update of the various strategies employed to assign a function to these receptors and to discover new ligands. We focus on the recent advances in the identification of endogenous ligands with a detailed description of newly deorphanized receptors. Replication being a key parameter in these endeavors, we also discuss the latest controversies about problematic ligand-receptor pairings. In this context, we propose several recommendations in order to strengthen the reporting of new ligand-receptor pairs.
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39
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Izquierdo C, Gómez-Tamayo JC, Nebel JC, Pardo L, Gonzalez A. Identifying human diamine sensors for death related putrescine and cadaverine molecules. PLoS Comput Biol 2018; 14:e1005945. [PMID: 29324768 PMCID: PMC5783396 DOI: 10.1371/journal.pcbi.1005945] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 01/24/2018] [Accepted: 12/28/2017] [Indexed: 12/21/2022] Open
Abstract
Pungent chemical compounds originating from decaying tissue are strong drivers of animal behavior. Two of the best-characterized death smell components are putrescine (PUT) and cadaverine (CAD), foul-smelling molecules produced by decarboxylation of amino acids during decomposition. These volatile polyamines act as ‘necromones’, triggering avoidance or attractive responses, which are fundamental for the survival of a wide range of species. The few studies that have attempted to identify the cognate receptors for these molecules have suggested the involvement of the seven-helix trace amine-associated receptors (TAARs), localized in the olfactory epithelium. However, very little is known about the precise chemosensory receptors that sense these compounds in the majority of organisms and the molecular basis of their interactions. In this work, we have used computational strategies to characterize the binding between PUT and CAD with the TAAR6 and TAAR8 human receptors. Sequence analysis, homology modeling, docking and molecular dynamics studies suggest a tandem of negatively charged aspartates in the binding pocket of these receptors which are likely to be involved in the recognition of these small biogenic diamines. The distinctive dead smell comes largely from molecules like cadaverine and putrescine that are produced during decomposition of organic tissues. These volatile compounds act as powerful chemical signals important for the survival of a wide range of species. Previous studies have identified the trace amine-associated receptor 13c (or TAAR13c) in zebrafish as the cognate receptor of cadaverine in bony fishes. In this work, we employed computational strategies to disclose the human TAAR6 and TAAR8 receptors as sensors of the putrescine and cadaverine molecules. Our results indicate that several negatively charged residues in the ligand binding pocket of these receptors constitute the molecular basis for recognition of these necromones in humans.
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Affiliation(s)
- Cristina Izquierdo
- Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Spain
| | - José C. Gómez-Tamayo
- Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Spain
| | - Jean-Christophe Nebel
- Faculty of Science, Engineering and Computing, Kingston University, London, United Kingdom
| | - Leonardo Pardo
- Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Spain
| | - Angel Gonzalez
- Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Spain
- * E-mail:
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Rucktooa P, Cheng RKY, Segala E, Geng T, Errey JC, Brown GA, Cooke RM, Marshall FH, Doré AS. Towards high throughput GPCR crystallography: In Meso soaking of Adenosine A 2A Receptor crystals. Sci Rep 2018; 8:41. [PMID: 29311713 PMCID: PMC5758569 DOI: 10.1038/s41598-017-18570-w] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 12/08/2017] [Indexed: 01/14/2023] Open
Abstract
Here we report an efficient method to generate multiple co-structures of the A2A G protein-coupled receptor (GPCR) with small-molecules from a single preparation of a thermostabilised receptor crystallised in Lipidic Cubic Phase (LCP). Receptor crystallisation is achieved following purification using a low affinity “carrier” ligand (theophylline) and crystals are then soaked in solutions containing the desired (higher affinity) compounds. Complete datasets to high resolution can then be collected from single crystals and seven structures are reported here of which three are novel. The method significantly improves structural throughput for ligand screening using stabilised GPCRs, thereby actively driving Structure-Based Drug Discovery (SBDD).
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Affiliation(s)
- Prakash Rucktooa
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire, AL7 3AX, UK
| | - Robert K Y Cheng
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire, AL7 3AX, UK.,LeadXpro, Park InnovAARE, 5232, Villigen, Switzerland
| | - Elena Segala
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire, AL7 3AX, UK
| | - Tian Geng
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire, AL7 3AX, UK
| | - James C Errey
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire, AL7 3AX, UK
| | - Giles A Brown
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire, AL7 3AX, UK
| | - Robert M Cooke
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire, AL7 3AX, UK
| | - Fiona H Marshall
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire, AL7 3AX, UK.
| | - Andrew S Doré
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire, AL7 3AX, UK
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Abstract
Advances in the structural biology of G-protein Coupled Receptors have resulted in a significant step forward in our understanding of how this important class of drug targets function at the molecular level. However, it has also become apparent that they are very dynamic molecules, and moreover, that the underlying dynamics is crucial in shaping the response to different ligands. Molecular dynamics simulations can provide unique insight into the dynamic properties of GPCRs in a way that is complementary to many experimental approaches. In this chapter, we describe progress in three distinct areas that are particularly difficult to study with other techniques: atomic level investigation of the conformational changes that occur when moving between the various states that GPCRs can exist in, the pathways that ligands adopt during binding/unbinding events and finally, the influence of lipids on the conformational dynamics of GPCRs.
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Affiliation(s)
- Naushad Velgy
- Department of Biochemistry, Structural Bioinformatics and Computational Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - George Hedger
- Department of Biochemistry, Structural Bioinformatics and Computational Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Philip C Biggin
- Department of Biochemistry, Structural Bioinformatics and Computational Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
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Zhang XJ, Cheng X, Yan ZZ, Fang J, Wang X, Wang W, Liu ZY, Shen LJ, Zhang P, Wang PX, Liao R, Ji YX, Wang JY, Tian S, Zhu XY, Zhang Y, Tian RF, Wang L, Ma XL, Huang Z, She ZG, Li H. An ALOX12–12-HETE–GPR31 signaling axis is a key mediator of hepatic ischemia–reperfusion injury. Nat Med 2017; 24:73-83. [DOI: 10.1038/nm.4451] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 11/01/2017] [Indexed: 12/12/2022]
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Wu Z, Lu W, Yu W, Wang T, Li W, Liu G, Zhang H, Pang X, Huang J, Liu M, Cheng F, Tang Y. Quantitative and systems pharmacology 2. In silico polypharmacology of G protein-coupled receptor ligands via network-based approaches. Pharmacol Res 2017; 129:400-413. [PMID: 29133212 DOI: 10.1016/j.phrs.2017.11.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 11/07/2017] [Accepted: 11/07/2017] [Indexed: 02/06/2023]
Abstract
G protein-coupled receptors (GPCRs) are the largest super family with more than 800 membrane receptors. Currently, over 30% of the approved drugs target human GPCRs. However, only approximately 30 human GPCRs have been resolved three-dimensional crystal structures, which limits traditional structure-based drug discovery. Recent advances in network-based systems pharmacology approaches have demonstrated powerful strategies for identifying new targets of GPCR ligands. In this study, we proposed a network-based systems pharmacology framework for comprehensive identification of new drug-target interactions on GPCRs. Specifically, we reconstructed both global and local drug-target interaction networks for human GPCRs. Network analysis on the known drug-target networks showed rational strategies for designing new GPCR ligands and evaluating side effects of the approved GPCR drugs. We further built global and local network-based models for predicting new targets of the known GPCR ligands. The area under the receiver operating characteristic curve of more than 0.96 was obtained for the best network-based models in cross validation. In case studies, we identified that several network-predicted GPCR off-targets (e.g. ADRA2A, ADRA2C and CHRM2) were associated with cardiovascular complications (e.g. bradycardia and palpitations) of the approved GPCR drugs via an integrative analysis of drug-target and off-target-adverse drug event networks. Importantly, we experimentally validated that two newly predicted compounds, AM966 and Ki16425, showed high binding affinities on prostaglandin E2 receptor EP4 subtype with IC50=2.67μM and 6.34μM, respectively. In summary, this study offers powerful network-based tools for identifying polypharmacology of GPCR ligands in drug discovery and development.
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Affiliation(s)
- Zengrui Wu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Weiqiang Lu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Weiwei Yu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Tianduanyi Wang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Weihua Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Guixia Liu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Hankun Zhang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Xiufeng Pang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jin Huang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Mingyao Liu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China; Institute of Biosciences and Technology, Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center, Houston, TX 77030, USA.
| | - Feixiong Cheng
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Center for Complex Networks Research, Northeastern University, Boston, MA 02115, USA.
| | - Yun Tang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China.
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Gacasan SB, Baker DL, Parrill AL. G protein-coupled receptors: the evolution of structural insight. AIMS BIOPHYSICS 2017; 4:491-527. [PMID: 29951585 DOI: 10.3934/biophy.2017.3.491] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
G protein-coupled receptors (GPCR) comprise a diverse superfamily of over 800 proteins that have gained relevance as biological targets for pharmaceutical drug design. Although these receptors have been investigated for decades, three-dimensional structures of GPCR have only recently become available. In this review, we focus on the technological advancements that have facilitated efforts to gain insights into GPCR structure. Progress in these efforts began with the initial crystal structure determination of rhodopsin (PDB: 1F88) in 2000 and has continued to the most recently published structure of the A1AR (PDB: 5UEN) in 2017. Numerous experimental developments over the past two decades have opened the door for widespread GPCR structural characterization. These efforts have resulted in the determination of three-dimensional structures for over 40 individual GPCR family members. Herein we present a comprehensive list and comparative analysis of over 180 individual GPCR structures. This includes a summary of different GPCR functional states crystallized with agonists, dual agonists, partial agonists, inverse agonists, antagonists, and allosteric modulators.
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Affiliation(s)
- Samantha B Gacasan
- Department of Chemistry, University of Memphis, 3744 Walker Ave, Memphis, TN 38152, USA
| | - Daniel L Baker
- Department of Chemistry, University of Memphis, 3744 Walker Ave, Memphis, TN 38152, USA
| | - Abby L Parrill
- Department of Chemistry, University of Memphis, 3744 Walker Ave, Memphis, TN 38152, USA
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Lee Y, Basith S, Choi S. Recent Advances in Structure-Based Drug Design Targeting Class A G Protein-Coupled Receptors Utilizing Crystal Structures and Computational Simulations. J Med Chem 2017; 61:1-46. [PMID: 28657745 DOI: 10.1021/acs.jmedchem.6b01453] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
G protein-coupled receptors (GPCRs) represent the largest and most physiologically important integral membrane protein family, and these receptors respond to a wide variety of physiological and environmental stimuli. GPCRs are among the most critical therapeutic targets for numerous human diseases, and approximately one-third of the currently marketed drugs target this receptor family. The recent breakthroughs in GPCR structural biology have significantly contributed to our understanding of GPCR function, ligand binding, and pharmacological action as well as to the design of new drugs. This perspective highlights the latest advances in GPCR structures with a focus on the receptor-ligand interactions of each receptor family in class A nonrhodopsin GPCRs as well as the structural features for their activation, biased signaling, and allosteric mechanisms. The current state-of-the-art methodologies of structure-based drug design (SBDD) approaches in the GPCR research field are also discussed.
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Affiliation(s)
- Yoonji Lee
- National Leading Research Laboratory (NLRL) of Molecular Modeling & Drug Design, College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University , Seoul 03760, Republic of Korea
| | - Shaherin Basith
- National Leading Research Laboratory (NLRL) of Molecular Modeling & Drug Design, College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University , Seoul 03760, Republic of Korea
| | - Sun Choi
- National Leading Research Laboratory (NLRL) of Molecular Modeling & Drug Design, College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University , Seoul 03760, Republic of Korea
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46
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Structural insights into the extracellular recognition of the human serotonin 2B receptor by an antibody. Proc Natl Acad Sci U S A 2017; 114:8223-8228. [PMID: 28716900 DOI: 10.1073/pnas.1700891114] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Monoclonal antibodies provide an attractive alternative to small-molecule therapies for a wide range of diseases. Given the importance of G protein-coupled receptors (GPCRs) as pharmaceutical targets, there has been an immense interest in developing therapeutic monoclonal antibodies that act on GPCRs. Here we present the 3.0-Å resolution structure of a complex between the human 5-hydroxytryptamine 2B (5-HT2B) receptor and an antibody Fab fragment bound to the extracellular side of the receptor, determined by serial femtosecond crystallography with an X-ray free-electron laser. The antibody binds to a 3D epitope of the receptor that includes all three extracellular loops. The 5-HT2B receptor is captured in a well-defined active-like state, most likely stabilized by the crystal lattice. The structure of the complex sheds light on the mechanism of selectivity in extracellular recognition of GPCRs by monoclonal antibodies.
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47
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Martin-Garcia JM, Conrad CE, Nelson G, Stander N, Zatsepin NA, Zook J, Zhu L, Geiger J, Chun E, Kissick D, Hilgart MC, Ogata C, Ishchenko A, Nagaratnam N, Roy-Chowdhury S, Coe J, Subramanian G, Schaffer A, James D, Ketwala G, Venugopalan N, Xu S, Corcoran S, Ferguson D, Weierstall U, Spence JCH, Cherezov V, Fromme P, Fischetti RF, Liu W. Serial millisecond crystallography of membrane and soluble protein microcrystals using synchrotron radiation. IUCRJ 2017; 4:439-454. [PMID: 28875031 PMCID: PMC5571807 DOI: 10.1107/s205225251700570x] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 04/13/2017] [Indexed: 05/17/2023]
Abstract
Crystal structure determination of biological macromolecules using the novel technique of serial femtosecond crystallography (SFX) is severely limited by the scarcity of X-ray free-electron laser (XFEL) sources. However, recent and future upgrades render microfocus beamlines at synchrotron-radiation sources suitable for room-temperature serial crystallography data collection also. Owing to the longer exposure times that are needed at synchrotrons, serial data collection is termed serial millisecond crystallography (SMX). As a result, the number of SMX experiments is growing rapidly, with a dozen experiments reported so far. Here, the first high-viscosity injector-based SMX experiments carried out at a US synchrotron source, the Advanced Photon Source (APS), are reported. Microcrystals (5-20 µm) of a wide variety of proteins, including lysozyme, thaumatin, phycocyanin, the human A2A adenosine receptor (A2AAR), the soluble fragment of the membrane lipoprotein Flpp3 and proteinase K, were screened. Crystals suspended in lipidic cubic phase (LCP) or a high-molecular-weight poly(ethylene oxide) (PEO; molecular weight 8 000 000) were delivered to the beam using a high-viscosity injector. In-house data-reduction (hit-finding) software developed at APS as well as the SFX data-reduction and analysis software suites Cheetah and CrystFEL enabled efficient on-site SMX data monitoring, reduction and processing. Complete data sets were collected for A2AAR, phycocyanin, Flpp3, proteinase K and lysozyme, and the structures of A2AAR, phycocyanin, proteinase K and lysozyme were determined at 3.2, 3.1, 2.65 and 2.05 Å resolution, respectively. The data demonstrate the feasibility of serial millisecond crystallography from 5-20 µm crystals using a high-viscosity injector at APS. The resolution of the crystal structures obtained in this study was dictated by the current flux density and crystal size, but upcoming developments in beamline optics and the planned APS-U upgrade will increase the intensity by two orders of magnitude. These developments will enable structure determination from smaller and/or weakly diffracting microcrystals.
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Affiliation(s)
- Jose M. Martin-Garcia
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Chelsie E. Conrad
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Garrett Nelson
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, PO Box 871504, Tempe, AZ 85287, USA
| | - Natasha Stander
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, PO Box 871504, Tempe, AZ 85287, USA
| | - Nadia A. Zatsepin
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, PO Box 871504, Tempe, AZ 85287, USA
| | - James Zook
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Lan Zhu
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - James Geiger
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Eugene Chun
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - David Kissick
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
| | - Mark C. Hilgart
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
| | - Craig Ogata
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
| | - Andrii Ishchenko
- Department of Chemistry, Bridge Institute, University of Southern California, 3430 South Vermont Avenue, MC 3303, Los Angeles, CA 90089, USA
| | - Nirupa Nagaratnam
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Shatabdi Roy-Chowdhury
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Jesse Coe
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Ganesh Subramanian
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, PO Box 871504, Tempe, AZ 85287, USA
| | - Alexander Schaffer
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Daniel James
- Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Gihan Ketwala
- Department of Physics, Arizona State University, PO Box 871504, Tempe, AZ 85287, USA
| | - Nagarajan Venugopalan
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
| | - Shenglan Xu
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
| | - Stephen Corcoran
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
| | - Dale Ferguson
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
| | - Uwe Weierstall
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, PO Box 871504, Tempe, AZ 85287, USA
| | - John C. H. Spence
- Department of Physics, Arizona State University, PO Box 871504, Tempe, AZ 85287, USA
| | - Vadim Cherezov
- Department of Chemistry, Bridge Institute, University of Southern California, 3430 South Vermont Avenue, MC 3303, Los Angeles, CA 90089, USA
| | - Petra Fromme
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Robert F. Fischetti
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
| | - Wei Liu
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
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