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Jann C, Giofré S, Bhattacharjee R, Lemke EA. Cracking the Code: Reprogramming the Genetic Script in Prokaryotes and Eukaryotes to Harness the Power of Noncanonical Amino Acids. Chem Rev 2024. [PMID: 39120726 DOI: 10.1021/acs.chemrev.3c00878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2024]
Abstract
Over 500 natural and synthetic amino acids have been genetically encoded in the last two decades. Incorporating these noncanonical amino acids into proteins enables many powerful applications, ranging from basic research to biotechnology, materials science, and medicine. However, major challenges remain to unleash the full potential of genetic code expansion across disciplines. Here, we provide an overview of diverse genetic code expansion methodologies and systems and their final applications in prokaryotes and eukaryotes, represented by Escherichia coli and mammalian cells as the main workhorse model systems. We highlight the power of how new technologies can be first established in simple and then transferred to more complex systems. For example, whole-genome engineering provides an excellent platform in bacteria for enabling transcript-specific genetic code expansion without off-targets in the transcriptome. In contrast, the complexity of a eukaryotic cell poses challenges that require entirely new approaches, such as striving toward establishing novel base pairs or generating orthogonally translating organelles within living cells. We connect the milestones in expanding the genetic code of living cells for encoding novel chemical functionalities to the most recent scientific discoveries, from optimizing the physicochemical properties of noncanonical amino acids to the technological advancements for their in vivo incorporation. This journey offers a glimpse into the promising developments in the years to come.
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Affiliation(s)
- Cosimo Jann
- Biocenter, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
- IMB Postdoc Programme (IPPro), 55128 Mainz, Germany
| | - Sabrina Giofré
- Biocenter, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
- IMB Postdoc Programme (IPPro), 55128 Mainz, Germany
| | - Rajanya Bhattacharjee
- Biocenter, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
- IMB International PhD Programme (IPP), 55128 Mainz, Germany
| | - Edward A Lemke
- Biocenter, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
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2
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Huang YH, Lin SY, Ou LC, Huang WC, Chao PK, Chang YC, Chang HF, Lee PT, Yeh TK, Kuo YH, Tien YW, Xi JH, Tao PL, Chen PY, Chuang JY, Shih C, Chen CT, Tung CW, Loh HH, Ueng SH, Yeh SH. Discovery of a mu-opioid receptor modulator that in combination with morphinan antagonists induces analgesia. Cell Chem Biol 2024:S2451-9456(24)00272-1. [PMID: 39025070 DOI: 10.1016/j.chembiol.2024.06.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 04/09/2024] [Accepted: 06/22/2024] [Indexed: 07/20/2024]
Abstract
Morphinan antagonists, which block opioid effects at mu-opioid receptors, have been studied for their analgesic potential. Previous studies have suggested that these antagonists elicit analgesia with fewer adverse effects in the presence of the mutant mu-opioid receptor (MOR; S196A). However, introducing a mutant receptor for medical applications represents significant challenges. We hypothesize that binding a chemical compound to the MOR may elicit a comparable effect to the S196A mutation. Through high-throughput screening and structure-activity relationship studies, we identified a modulator, 4-(2-(4-fluorophenyl)-4-oxothiazolidin-3-yl)-3-methylbenzoic acid (BPRMU191), which confers agonistic properties to small-molecule morphinan antagonists, which induce G protein-dependent MOR activation. Co-application of BPRMU191 and morphinan antagonists resulted in MOR-dependent analgesia with diminished side effects, including gastrointestinal dysfunction, antinociceptive tolerance, and physical and psychological dependence. Combining BPRMU191 and morphinan antagonists could serve as a potential therapeutic strategy for severe pain with reduced adverse effects and provide an avenue for studying G protein-coupled receptor modulation.
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Affiliation(s)
- Yi-Han Huang
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli 35053, Taiwan; Research Center for Neuroscience, Taipei Medical University, Taipei 110, Taiwan
| | - Shu-Yu Lin
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli 35053, Taiwan
| | - Li-Chin Ou
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli 35053, Taiwan
| | - Wei-Cheng Huang
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli 35053, Taiwan
| | - Po-Kuan Chao
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli 35053, Taiwan
| | - Yung-Chiao Chang
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli 35053, Taiwan
| | - Hsiao-Fu Chang
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli 35053, Taiwan
| | - Pin-Tse Lee
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli 35053, Taiwan
| | - Teng-Kuang Yeh
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli 35053, Taiwan
| | - Yu-Hsien Kuo
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli 35053, Taiwan
| | - Ya-Wen Tien
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli 35053, Taiwan
| | - Jing-Hua Xi
- Department of Pharmacology, Medical School University of Minnesota, Minneapolis, MN 55455-0217, USA
| | - Pao-Luh Tao
- Center for Neuropsychiatric Research, National Health Research Institutes, Miaoli 35053, Taiwan
| | - Pin-Yuan Chen
- Department of Neurosurgery, Keelung Chang Gung Memorial Hospital, Chang Gung University, Keelung 20401, Taiwan
| | - Jian-Ying Chuang
- Research Center for Neuroscience, Taipei Medical University, Taipei 110, Taiwan; Ph.D. Program in Medical Neuroscience, College of Medical Science and Technology, Taipei Medical University and National Health Research Institutes, Taipei 110, Taiwan
| | - Chuan Shih
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli 35053, Taiwan
| | - Chiung-Tong Chen
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli 35053, Taiwan
| | - Chun-Wei Tung
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli 35053, Taiwan
| | - Horace H Loh
- Department of Pharmacology, Medical School University of Minnesota, Minneapolis, MN 55455-0217, USA; Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China.
| | - Shau-Hua Ueng
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli 35053, Taiwan; School of Pharmacy, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan.
| | - Shiu-Hwa Yeh
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli 35053, Taiwan; Ph.D. Program in Medical Neuroscience, College of Medical Science and Technology, Taipei Medical University and National Health Research Institutes, Taipei 110, Taiwan.
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3
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Mattheisen JM, Wollowitz JS, Huber T, Sakmar TP. Genetic code expansion to enable site-specific bioorthogonal labeling of functional G protein-coupled receptors in live cells. Protein Sci 2023; 32:e4550. [PMID: 36540928 PMCID: PMC9847076 DOI: 10.1002/pro.4550] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/13/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022]
Abstract
For use in site-specific bioorthogonal labeling of expressed G protein-coupled receptors (GPCRs) in live cells, we developed a luciferase-based reporter assay. The assay was used to compare amber codon suppression efficiency, receptor functionality, and efficiency of different bioorthogonal labeling chemistries. We used the assay system to compare side-by-side the efficiency of incorporation of three different noncanonical amino acids [4-azido-l-phenylalanine (azF), cyclopropene-l-lysine (CpK), and trans-cyclooct-2-en-l-lysine (TCOK)] at three different sites on a GPCR using three different genetic code expansion plasmid systems. As a model GPCR, we engineered an epitope-tagged C-C chemokine receptor 5 (CCR5)-RLuc3 fusion for expression in HEK293T cells. Satisfactory incorporation of azF, CpK, and TCOK into heterologously expressed CCR5 was achieved. We also carried out cell-based calcium mobilization assays to measure the function of the engineered CCR5, and in the same cells, we performed bioorthogonal labeling of the engineered mutants using heterobivalent compounds containing bioorthogonal tethering groups linked to either a small-molecule fluorophore or a peptide. Favorable reaction kinetics of tetrazine-containing compounds with CCR5 harboring TCOK was observed. However, bioorthogonal labeling in live cells of CCR5 harboring CpK with tetrazine-containing compounds using the inverse electron demand Diels-Alder ligation was overall slightly more efficient than other reactions tested.
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Affiliation(s)
- Jordan M. Mattheisen
- Laboratory of Chemical Biology and Signal TransductionThe Rockefeller UniversityNew YorkNew YorkUSA
- Tri‐Institutional PhD Program in Chemical BiologyNew YorkNew YorkUSA
| | - Jaina S. Wollowitz
- Laboratory of Chemical Biology and Signal TransductionThe Rockefeller UniversityNew YorkNew YorkUSA
- Tri‐Institutional PhD Program in Chemical BiologyNew YorkNew YorkUSA
| | - Thomas Huber
- Laboratory of Chemical Biology and Signal TransductionThe Rockefeller UniversityNew YorkNew YorkUSA
| | - Thomas P. Sakmar
- Laboratory of Chemical Biology and Signal TransductionThe Rockefeller UniversityNew YorkNew YorkUSA
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4
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Shin G, Lim SI. Unveiling the biological interface of protein complexes by mass spectrometry-coupled methods. Proteins 2022; 91:593-607. [PMID: 36573681 DOI: 10.1002/prot.26459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 11/28/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022]
Abstract
Most biomolecules become functional and bioactive by forming protein complexes through interaction with ligands that are diverse in size, shape, and physicochemical properties. In the complex biological milieu, the interaction is ligand-specific, driven by molecular sensing, and involves the recognition of a binding interface localized within a protein structure. Mapping interfaces of protein complexes is a highly sought area of research as it delivers fundamental insights into proteomes and pathology and hence strategies for therapeutics. While X-ray crystallography and electron microscopy remain the gold standard for structural elucidation of protein complexes, their artificial and static analytic nature often produces a non-native interface that otherwise might be negligible or non-existent in a biological environment. Recently, the mass spectrometry-coupled approaches, chemical crosslinking (CLMS) and hydrogen-deuterium exchange (HDMS) have become valuable analytic complements to the traditional techniques. These methods explicitly identify hot residues and motifs embedded in binding interfaces, especially when the interaction is predominantly dynamic, transient, and/or caused by an intrinsically disordered domain. Here, we review the principal role of CLMS and HDMS in protein structural biology with a particular emphasis on the contribution of recent examples to exploring biological interfaces. Additionally, we describe recent studies that utilized these methods to expand our understanding of protein complex formation and the related biological processes, to increase the probability of structure-based drug design.
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Affiliation(s)
- Goeun Shin
- Department of Chemical Engineering, Pukyong National University, Busan, South Korea
| | - Sung In Lim
- Department of Chemical Engineering, Pukyong National University, Busan, South Korea
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5
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Ulvan inhibits α-synuclein fibrillation and disrupts the mature fibrils: In vitro and in vivo studies. Int J Biol Macromol 2022; 211:580-591. [PMID: 35561861 DOI: 10.1016/j.ijbiomac.2022.05.045] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 05/02/2022] [Accepted: 05/06/2022] [Indexed: 11/24/2022]
Abstract
Misfolding and aggregation of α-synuclein (α-syn) play a key role in the pathogenesis of Parkinson's disease (PD). Herein, the inhibitory effect of ulvan on α-syn fibrillogenesis was studied using thioflavin T fluorescence and atomic force microscope assays. It is shown that ulvan could inhibit α-syn fibrillogenesis in a dose-dependent manner. Based on the circular dichroism results, it is found that ulvan delays greatly the conformational transition from its initial random coil to β-sheet rich structure. The protective effect of ulvan against celllular death induced by α-syn aggregates was investigated by MTT colorimetric and cellular staining methods. It is found that ulvan protects greatly PC12 cells from α-syn fibril-induced cytotoxicity. In addition, ulvan disaggregates preformed α-syn fibrils and reduces cytotoxicity in a dose-dependent manner. Thereafter, the inhibitory effects of ulvan against α-syn fibrillogenesis were probed using Caenorhabditis elegans model NL5901 expressing human α-syn. It is found that ulvan extends the lifespan of NL5901 and recovers the lipid deposition by reducing the accumulation of α-syn. Finally, the molecular interactions between ulvan and α-syn pentamer was also explored using molecular docking. These findings suggest that ulvan can be pursued as a novel candidate drug for treatment of PD.
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6
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Joest EF, Winter C, Wesalo JS, Deiters A, Tampé R. Efficient Amber Suppression via Ribosomal Skipping for In Situ Synthesis of Photoconditional Nanobodies. ACS Synth Biol 2022; 11:1466-1476. [PMID: 35060375 PMCID: PMC9157392 DOI: 10.1021/acssynbio.1c00471] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Genetic code expansion is a versatile method for in situ synthesis of modified proteins. During mRNA translation, amber stop codons are suppressed to site-specifically incorporate non-canonical amino acids. Thus, nanobodies can be equipped with photocaged amino acids to control target binding on demand. The efficiency of amber suppression and protein synthesis can vary with unpredictable background expression, and the reasons are hardly understood. Here, we identified a substantial limitation that prevented synthesis of nanobodies with N-terminal modifications for light control. After systematic analyses, we hypothesized that nanobody synthesis was severely affected by ribosomal inaccuracy during the early phases of translation. To circumvent a background-causing read-through of a premature stop codon, we designed a new suppression concept based on ribosomal skipping. As an example, we generated intrabodies with photoactivated target binding in mammalian cells. The findings provide valuable insights into the genetic code expansion and describe a versatile synthesis route for the generation of modified nanobodies that opens up new perspectives for efficient site-specific integration of chemical tools. In the area of photopharmacology, our flexible intrabody concept builds an ideal platform to modulate target protein function and interaction.
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Affiliation(s)
- Eike F Joest
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M, Germany
| | - Christian Winter
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M, Germany
| | - Joshua S Wesalo
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M, Germany
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7
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Rudolf S, Kaempf K, Vu O, Meiler J, Beck‐Sickinger AG, Coin I. Binding of Natural Peptide Ligands to the Neuropeptide Y
5
Receptor. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202108738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Sarina Rudolf
- Institute of Biochemistry Faculty of Life Science Leipzig University 04103 Leipzig Germany
| | - Kerstin Kaempf
- Institute of Biochemistry Faculty of Life Science Leipzig University 04103 Leipzig Germany
| | - Oanh Vu
- Chemistry Department Vanderbilt University Nashville TN 37212 USA
| | - Jens Meiler
- Chemistry Department Vanderbilt University Nashville TN 37212 USA
- Center for Structural Biology Department of Biological Sciences Vanderbilt University Nashville TN 37212 USA
- Institute of Drug Design Faculty of Medicine Leipzig University 04103 Leipzig Germany
| | | | - Irene Coin
- Institute of Biochemistry Faculty of Life Science Leipzig University 04103 Leipzig Germany
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8
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Rudolf S, Kaempf K, Vu O, Meiler J, Beck-Sickinger AG, Coin I. Binding of Natural Peptide Ligands to the Neuropeptide Y 5 Receptor. Angew Chem Int Ed Engl 2022; 61:e202108738. [PMID: 34822209 PMCID: PMC8766924 DOI: 10.1002/anie.202108738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Indexed: 01/28/2023]
Abstract
The binding mode of natural peptide ligands to the Y5 G protein-coupled receptor (Y5 R), an attractive therapeutic target for the treatment of obesity, is largely unknown. Here, we apply complementary biochemical and computational approaches, including scanning of the receptor surface with a genetically encoded crosslinker, Ala-scanning of the ligand and double-cycle mutagenesis, to map interactions in the ligand-receptor interface and build a structural model of the NPY-Y5 R complex guided by the experimental data. In the model, the carboxyl (C)-terminus of bound NPY is placed close to the extracellular loop (ECL) 3, whereas the characteristic α-helical segment of the ligand drapes over ECL1 and is tethered towards ECL2 by a hydrophobic cluster. We further show that the other two natural ligands of Y5 R, peptide YY (PYY) and pancreatic polypeptide (PP) dock to the receptor in a similar pose.
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Affiliation(s)
- Sarina Rudolf
- Institute of Biochemistry, Faculty of Life Science, Leipzig University, Leipzig 04103, Germany
| | - Kerstin Kaempf
- Institute of Biochemistry, Faculty of Life Science, Leipzig University, Leipzig 04103, Germany
| | - Oanh Vu
- Chemistry Department, Vanderbilt University, Nashville, Tennessee 37212, U.S.A
| | - Jens Meiler
- Chemistry Department, Vanderbilt University, Nashville, Tennessee 37212, U.S.A
- Center for Structural Biology, Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37212, U.S.A
- Institute of Drug Design, Faculty of Medicine, Leipzig University, Leipzig 04103, Germany
| | | | - Irene Coin
- Institute of Biochemistry, Faculty of Life Science, Leipzig University, Leipzig 04103, Germany
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9
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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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10
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Gagnon L, Cao Y, Cho A, Sedki D, Huber T, Sakmar TP, Laporte SA. Genetic code expansion and photocross-linking identify different β-arrestin binding modes to the angiotensin II type 1 receptor. J Biol Chem 2019; 294:17409-17420. [PMID: 31530642 DOI: 10.1074/jbc.ra119.010324] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 09/05/2019] [Indexed: 12/28/2022] Open
Abstract
The angiotensin II (AngII) type 1 receptor (AT1R) is a member of the G protein-coupled receptor (GPCR) family and binds β-arrestins (β-arrs), which regulate AT1R signaling and trafficking. These processes can be biased by different ligands or mutations in the AGTR1 gene. As for many GPCRs, the exact details for AT1R-β-arr interactions driven by AngII or β-arr-biased ligands remain largely unknown. Here, we used the amber-suppression technology to site-specifically introduce the unnatural amino acid (UAA) p-azido-l-phenylalanine (azF) into the intracellular loops (ICLs) and the C-tail of AT1R. Our goal was to generate competent photoreactive receptors that can be cross-linked to β-arrs in cells. We performed UV-mediated photolysis of 25 different azF-labeled AT1Rs to cross-link β-arr1 to AngII-bound receptors, enabling us to map important contact sites in the C-tail and in the ICL2 and ICL3 of the receptor. The extent of AT1R-β-arr1 cross-linking among azF-labeled receptors differed, revealing variability in β-arr's contact mode with the different AT1R domains. Moreover, the signature of ligated AT1R-β-arr complexes from a subset of azF-labeled receptors also differed between AngII and β-arr-biased ligand stimulation of receptors and between azF-labeled AT1R bearing and that lacking a bias signaling mutation. These observations further implied distinct interaction modalities of the AT1R-β-arr1 complex in biased signaling conditions. Our findings demonstrate that this photocross-linking approach is useful for understanding GPCR-β-arr complexes in different activation states and could be extended to study other protein-protein interactions in cells.
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Affiliation(s)
- Laurence Gagnon
- Department of Medicine, Research Institute of the McGill University Health Center, McGill University, Montréal, Québec H4A 3J1, Canada
| | - Yubo Cao
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec H3G 1Y6, Canada
| | - Aaron Cho
- Department of Medicine, Research Institute of the McGill University Health Center, McGill University, Montréal, Québec H4A 3J1, Canada
| | - Dana Sedki
- Department of Medicine, Research Institute of the McGill University Health Center, McGill University, Montréal, Québec H4A 3J1, Canada
| | - Thomas Huber
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York 10065
| | - Thomas P Sakmar
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York 10065
| | - Stéphane A Laporte
- Department of Medicine, Research Institute of the McGill University Health Center, McGill University, Montréal, Québec H4A 3J1, Canada .,Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec H3G 1Y6, Canada
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11
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Nödling AR, Spear LA, Williams TL, Luk LYP, Tsai YH. Using genetically incorporated unnatural amino acids to control protein functions in mammalian cells. Essays Biochem 2019; 63:237-266. [PMID: 31092687 PMCID: PMC6610526 DOI: 10.1042/ebc20180042] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 03/14/2019] [Accepted: 03/19/2019] [Indexed: 02/07/2023]
Abstract
Genetic code expansion allows unnatural (non-canonical) amino acid incorporation into proteins of interest by repurposing the cellular translation machinery. The development of this technique has enabled site-specific incorporation of many structurally and chemically diverse amino acids, facilitating a plethora of applications, including protein imaging, engineering, mechanistic and structural investigations, and functional regulation. Particularly, genetic code expansion provides great tools to study mammalian proteins, of which dysregulations often have important implications in health. In recent years, a series of methods has been developed to modulate protein function through genetically incorporated unnatural amino acids. In this review, we will first discuss the basic concept of genetic code expansion and give an up-to-date list of amino acids that can be incorporated into proteins in mammalian cells. We then focus on the use of unnatural amino acids to activate, inhibit, or reversibly modulate protein function by translational, optical or chemical control. The features of each approach will also be highlighted.
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Affiliation(s)
| | - Luke A Spear
- School of Chemistry, Cardiff University, Cardiff, Wales, United Kingdom
| | - Thomas L Williams
- School of Chemistry, Cardiff University, Cardiff, Wales, United Kingdom
| | - Louis Y P Luk
- School of Chemistry, Cardiff University, Cardiff, Wales, United Kingdom
| | - Yu-Hsuan Tsai
- School of Chemistry, Cardiff University, Cardiff, Wales, United Kingdom
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12
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Miyazaki R, Akiyama Y, Mori H. A photo-cross-linking approach to monitor protein dynamics in living cells. Biochim Biophys Acta Gen Subj 2019; 1864:129317. [PMID: 30851405 DOI: 10.1016/j.bbagen.2019.03.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 02/26/2019] [Accepted: 03/04/2019] [Indexed: 11/16/2022]
Abstract
BACKGROUND Proteins, which comprise one of the major classes of biomolecules that constitute a cell, interact with other cellular factors during both their biogenesis and functional states. Studying not only static but also transient interactions of proteins is important to understand their physiological roles and regulation mechanisms. However, only a limited number of methods are available to analyze the dynamic behaviors of proteins at the molecular level in a living cell. The site-directed in vivo photo-cross-linking approach is an elegant technique to capture protein interactions with high spatial resolution in a living cell. SCOPE OF REVIEW Here, we review the in vivo photo-cross-linking approach including its recent applications and the potential problems to be considered. We also introduce a new in vivo photo-cross-linking-based technique (PiXie) to study protein dynamics with high spatiotemporal resolution. MAJOR CONCLUSIONS In vivo photo-cross-linking enables us to capture weak/transient protein interactions with high spatial resolution, and allows for identification of interacting factors. Moreover, the PiXie approach can be used to monitor rapid folding/assembly processes of proteins in living cells. GENERAL SIGNIFICANCE In vivo photo-cross-linking is a simple method that has been used to analyze the dynamic interactions of many cellular proteins. Originally developed in Escherichia coli, this system has been extended to studies in various organisms, making it a fundamental technique for investigating dynamic protein interactions in many cellular processes. This article is part of a Special issue entitled "Novel major techniques for visualizing 'live' protein molecules" edited by Dr. Daisuke Kohda.
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Affiliation(s)
- Ryoji Miyazaki
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Yoshinori Akiyama
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Hiroyuki Mori
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan.
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13
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Britton ZT, London TB, Carrell J, Dosanjh B, Wilkinson T, Bowen MA, Wu H, Dall’Acqua WF, Marelli M, Mazor Y. Tag-on-Demand: exploiting amber codon suppression technology for the enrichment of high-expressing membrane protein cell lines. Protein Eng Des Sel 2019; 31:389-398. [DOI: 10.1093/protein/gzy032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 11/16/2018] [Accepted: 12/18/2018] [Indexed: 12/20/2022] Open
Affiliation(s)
- Zachary T Britton
- Antibody Discovery and Protein Engineering, MedImmune, Gaithersburg, MD, USA
| | - Timothy B London
- Antibody Discovery and Protein Engineering, MedImmune, Cambridge, UK
- Current affiliation: TC BioPharm Limited, Glasgow, UK
| | - Jeffrey Carrell
- Respiratory, Inflammation and Autoimmune, MedImmune, Gaithersburg, MD, USA
| | - Bhupinder Dosanjh
- Antibody Discovery and Protein Engineering, MedImmune, Cambridge, UK
| | - Trevor Wilkinson
- Antibody Discovery and Protein Engineering, MedImmune, Cambridge, UK
| | - Michael A Bowen
- Antibody Discovery and Protein Engineering, MedImmune, Gaithersburg, MD, USA
| | - Herren Wu
- Antibody Discovery and Protein Engineering, MedImmune, Gaithersburg, MD, USA
| | | | - Marcello Marelli
- Antibody Discovery and Protein Engineering, MedImmune, Gaithersburg, MD, USA
| | - Yariv Mazor
- Antibody Discovery and Protein Engineering, MedImmune, Gaithersburg, MD, USA
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14
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Krause BS, Kaufmann JCD, Kuhne J, Vierock J, Huber T, Sakmar TP, Gerwert K, Bartl FJ, Hegemann P. Tracking Pore Hydration in Channelrhodopsin by Site-Directed Infrared-Active Azido Probes. Biochemistry 2019; 58:1275-1286. [DOI: 10.1021/acs.biochem.8b01211] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Benjamin S. Krause
- Institut für Biologie, Experimentelle Biophysik, Humboldt-Universität zu Berlin, Invalidenstrasse 42, 10115 Berlin, Germany
| | - Joel C. D. Kaufmann
- Institut für Biologie, Biophysikalische Chemie, Humboldt-Universität zu Berlin, Invalidenstrasse 42, 10115 Berlin, Germany
- Institut für medizinische Physik und Biophysik, Charité-Universitätsmedizin, Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Jens Kuhne
- Lehrstuhl für Biophysik, Ruhr-Universität Bochum, Universitätsstrasse 150, 44801 Bochum, Germany
| | - Johannes Vierock
- Institut für Biologie, Experimentelle Biophysik, Humboldt-Universität zu Berlin, Invalidenstrasse 42, 10115 Berlin, Germany
| | - Thomas Huber
- Laboratory of Chemical Biology & Signal Transduction, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
| | - Thomas P. Sakmar
- Laboratory of Chemical Biology & Signal Transduction, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
- Department of Neurobiology, Care Sciences and Society, Division for Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Alfred Nobels Allé 23, 141 57 Huddinge, Sweden
| | - Klaus Gerwert
- Lehrstuhl für Biophysik, Ruhr-Universität Bochum, Universitätsstrasse 150, 44801 Bochum, Germany
| | - Franz J. Bartl
- Institut für Biologie, Biophysikalische Chemie, Humboldt-Universität zu Berlin, Invalidenstrasse 42, 10115 Berlin, Germany
- Institut für medizinische Physik und Biophysik, Charité-Universitätsmedizin, Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Peter Hegemann
- Institut für Biologie, Experimentelle Biophysik, Humboldt-Universität zu Berlin, Invalidenstrasse 42, 10115 Berlin, Germany
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15
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Nguyen TA, Cigler M, Lang K. Expanding the Genetic Code to Study Protein-Protein Interactions. Angew Chem Int Ed Engl 2018; 57:14350-14361. [PMID: 30144241 DOI: 10.1002/anie.201805869] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 08/20/2018] [Indexed: 12/19/2022]
Abstract
Protein-protein interactions are central to many biological processes. A considerable challenge consists however in understanding and deciphering when and how proteins interact, and this can be particularly difficult when interactions are weak and transient. The site-specific incorporation of unnatural amino acids (UAAs) that crosslink with nearby molecules in response to light provides a powerful tool for mapping transient protein-protein interactions and for defining the structure and topology of protein complexes both in vitro and in vivo. Complementary strategies consist in site-specific incorporation of UAAs bearing electrophilic moieties that react with natural nucleophilic amino acids in a proximity-dependent manner, thereby chemically stabilizing low-affinity interactions and providing additional constraints on distances and geometries in protein complexes. Herein, we review how UAAs bearing fine-tuned chemical moieties that react with proteins in their vicinity can be utilized to map, study, and characterize weak and transient protein-protein interactions in living systems.
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Affiliation(s)
- Tuan-Anh Nguyen
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Group of Synthetic Biochemistry, Technical University of Munich, Institute for Advanced Study, Lichtenbergstr. 4, 85748, Garching, Germany
| | - Marko Cigler
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Group of Synthetic Biochemistry, Technical University of Munich, Institute for Advanced Study, Lichtenbergstr. 4, 85748, Garching, Germany
| | - Kathrin Lang
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Group of Synthetic Biochemistry, Technical University of Munich, Institute for Advanced Study, Lichtenbergstr. 4, 85748, Garching, Germany
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16
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Nguyen TA, Cigler M, Lang K. Expanding the Genetic Code to Study Protein-Protein Interactions. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201805869] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Tuan-Anh Nguyen
- Center for Integrated Protein Science Munich (CIPSM); Department of Chemistry; Group of Synthetic Biochemistry; Technical University of Munich; Institute for Advanced Study; Lichtenbergstr. 4 85748 Garching Germany
| | - Marko Cigler
- Center for Integrated Protein Science Munich (CIPSM); Department of Chemistry; Group of Synthetic Biochemistry; Technical University of Munich; Institute for Advanced Study; Lichtenbergstr. 4 85748 Garching Germany
| | - Kathrin Lang
- Center for Integrated Protein Science Munich (CIPSM); Department of Chemistry; Group of Synthetic Biochemistry; Technical University of Munich; Institute for Advanced Study; Lichtenbergstr. 4 85748 Garching Germany
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17
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Serfling R, Seidel L, Böttke T, Coin I. Optimizing the Genetic Incorporation of Chemical Probes into GPCRs for Photo-crosslinking Mapping and Bioorthogonal Chemistry in Live Mammalian Cells. J Vis Exp 2018. [PMID: 29683449 DOI: 10.3791/57069] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The genetic incorporation of non-canonical amino acids (ncAAs) via amber stop codon suppression is a powerful technique to install artificial probes and reactive moieties onto proteins directly in the live cell. Each ncAA is incorporated by a dedicated orthogonal suppressor-tRNA/amino-acyl-tRNA-synthetase (AARS) pair that is imported into the host organism. The incorporation efficiency of different ncAAs can greatly differ, and be unsatisfactory in some cases. Orthogonal pairs can be improved by manipulating either the AARS or the tRNA. However, directed evolution of tRNA or AARS using large libraries and dead/alive selection methods are not feasible in mammalian cells. Here, a facile and robust fluorescence-based assay to evaluate the efficiency of orthogonal pairs in mammalian cells is presented. The assay allows screening tens to hundreds of AARS/tRNA variants with a moderate effort and within a reasonable time. Use of this assay to generate new tRNAs that significantly improve the efficiency of the pyrrolysine orthogonal system is described, along with the application of ncAAs to the study of G-protein coupled receptors (GPCRs), which are challenging objects for ncAA mutagenesis. First, by systematically incorporating a photo-crosslinking ncAA throughout the extracellular surface of a receptor, binding sites of different ligands on the intact receptor are mapped directly in the live cell. Second, by incorporating last-generation ncAAs into a GPCR, ultrafast catalyst-free receptor labeling with a fluorescent dye is demonstrated, which exploits bioorthogonal strain-promoted inverse Diels Alder cycloaddition (SPIEDAC) on the live cell. As ncAAs can be generally applied to any protein independently on its size, the method is of general interest for a number of applications. In addition, ncAA incorporation does not require any special equipment and is easily performed in standard biochemistry labs.
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Affiliation(s)
- Robert Serfling
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig
| | - Lisa Seidel
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig
| | - Thore Böttke
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig
| | - Irene Coin
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig;
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18
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Huber T, Sakmar TP. Probing Antibody Binding Sites on G Protein-Coupled Receptors Using Genetically Encoded Photo-Activatable Cross-Linkers. Methods Mol Biol 2018; 1785:65-75. [PMID: 29714012 DOI: 10.1007/978-1-4939-7841-0_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We describe a methodology to map epitopes of monoclonal antibodies that bind to G protein-coupled receptors (GPCRs). The method relies on an amber codon suppression strategy to genetically encode photo-activatable cross-linkers, such as p-azido-L-phenylalanine (azF) or p-benzoly-L-phenylalanine (BzF), in GPCRs expressed in mammalian cells in culture. Individual receptor variants that harbor a site-specific photo-crosslinker residue can be assayed for functional activity in standard cell-based assays. The interaction sites between the receptor variants and an antibody can be mapped by determining which of the azF or BzF residues cross-link to the antibody upon UV irradiation. A whole cell enzyme-linked immunosorbent assay (ELISA) is used to quantiate cross-linking efficiency. A binding "footprint" of the antibody of the surface of the receptor is obtained by comparing the sites of amino acid replacements that cause loss of antibody binding with those that create colvalent cross-links with bound antibody. The precision of the receptor-antibody binding-site map is determined by the number of mutants tested and whether or not high resolution crystal structures or homology models are available. The targeted photo-cross-linking method is complementary to loss-of-function mutagenesis and is especially useful to study anti-receptor antibodies with discontinuous epitopes.
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Affiliation(s)
- Thomas Huber
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, NY, USA
| | - Thomas P Sakmar
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, NY, USA.
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19
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Rannversson H, Andersen J, Bang-Andersen B, Strømgaard K. Mapping the Binding Site for Escitalopram and Paroxetine in the Human Serotonin Transporter Using Genetically Encoded Photo-Cross-Linkers. ACS Chem Biol 2017; 12:2558-2562. [PMID: 28910072 DOI: 10.1021/acschembio.7b00338] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In spite of the important role of the human serotonin transporter (hSERT) in depression treatment, the molecular details of how antidepressant drugs bind are still not completely understood, in particular those related to potential high- and low-affinity binding sites in hSERT. Here, we utilize amber codon suppression in hSERT to encode the photo-cross-linking unnatural amino acid p-azido-l-phenylalanine into the suggested high- and low-affinity binding sites. We then employ UV-induced cross-linking with azF to map the binding site of escitalopram and paroxetine, two prototypical selective serotonin reuptake inhibitors (SSRIs). We find that the two antidepressant drugs exclusively cross-link to azF incorporated at the high-affinity binding site of hSERT, while cross-linking is not observed at the low-affinity binding site. Combined with previous homology models and recent structural data on hSERT, our results provide important information to understand the molecular details of these clinical relevant binding sites.
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Affiliation(s)
- Hafsteinn Rannversson
- Center
for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, 2100 Copenhagen Ø, Denmark
| | - Jacob Andersen
- Center
for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, 2100 Copenhagen Ø, Denmark
| | | | - Kristian Strømgaard
- Center
for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, 2100 Copenhagen Ø, Denmark
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20
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Vannecke W, Ampe C, Van Troys M, Beltramo M, Madder A. Cross-Linking Furan-Modified Kisspeptin-10 to the KISS Receptor. ACS Chem Biol 2017; 12:2191-2200. [PMID: 28714670 DOI: 10.1021/acschembio.7b00396] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Chemical cross-linking is well-established for investigating protein-protein interactions. Traditionally, photo cross-linking is used but is associated with problems of selectivity and UV toxicity in a biological context. We here describe, with live cells and under normal growth conditions, selective cross-linking of a furan-modified peptide ligand to its membrane-presented receptor with zero toxicity, high efficiency, and spatio-specificity. Furan-modified kisspeptin-10 is covalently coupled to its glycosylated membrane receptor, GPR54(KISS1R). This newly expands the applicability of furan-mediated cross-linking not only to protein-protein cross-linking but also to cross-linking in situ. Moreover, in our earlier reports on nucleic acid interstrand cross-linking, furan activation required external triggers of oxidation (via addition of N-bromo succinimide or singlet oxygen). In contrast, we here show, for multiple cell lines, the spontaneous endogenous oxidation of the furan moiety with concurrent selective cross-link formation. We propose that reactive oxygen species produced by NADPH oxidase (NOX) enzymes form the cellular source establishing furan oxidation.
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Affiliation(s)
- Willem Vannecke
- Organic
and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan
281 S4, B-9000 Ghent, Belgium
- Department
of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, B-9000 Ghent, Belgium
| | - Christophe Ampe
- Department
of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, B-9000 Ghent, Belgium
| | - Marleen Van Troys
- Department
of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, B-9000 Ghent, Belgium
| | - Massimiliano Beltramo
- Equipe
Neuroendocrinologie Moleculaire de la Reproduction, Physiologie de
la Reproduction et des Comportements, Centre INRA Val de Loire, 37380 Nouzilly, France
| | - Annemieke Madder
- Organic
and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan
281 S4, B-9000 Ghent, Belgium
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21
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Koole C, Reynolds CA, Mobarec JC, Hick C, Sexton PM, Sakmar TP. Genetically encoded photocross-linkers determine the biological binding site of exendin-4 peptide in the N-terminal domain of the intact human glucagon-like peptide-1 receptor (GLP-1R). J Biol Chem 2017; 292:7131-7144. [PMID: 28283573 PMCID: PMC5409479 DOI: 10.1074/jbc.m117.779496] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 03/09/2017] [Indexed: 12/25/2022] Open
Abstract
The glucagon-like peptide-1 receptor (GLP-1R) is a key therapeutic target in the management of type II diabetes mellitus, with actions including regulation of insulin biosynthesis and secretion, promotion of satiety, and preservation of β-cell mass. Like most class B G protein-coupled receptors (GPCRs), there is limited knowledge linking biological activity of the GLP-1R with the molecular structure of an intact, full-length, and functional receptor·ligand complex. In this study, we have utilized genetic code expansion to site-specifically incorporate the photoactive amino acid p-azido-l-phenylalanine (azF) into N-terminal residues of a full-length functional human GLP-1R in mammalian cells. UV-mediated photolysis of azF was then carried out to induce targeted photocross-linking to determine the proximity of the azido group in the mutant receptor with the peptide exendin-4. Cross-linking data were compared directly with the crystal structure of the isolated N-terminal extracellular domain of the GLP-1R in complex with exendin(9-39), revealing both similarities as well as distinct differences in the mode of interaction. Generation of a molecular model to accommodate the photocross-linking constraints highlights the potential influence of environmental conditions on the conformation of the receptor·peptide complex, including folding dynamics of the peptide and formation of dimeric and higher order oligomeric receptor multimers. These data demonstrate that crystal structures of isolated receptor regions may not give a complete reflection of peptide/receptor interactions and should be combined with additional experimental constraints to reveal peptide/receptor interactions occurring in the dynamic, native, and full-length receptor state.
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Affiliation(s)
- Cassandra Koole
- From the Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York 10065
| | - Christopher A Reynolds
- the School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
| | - Juan C Mobarec
- the School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
| | - Caroline Hick
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia, and
| | - Patrick M Sexton
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia, and
| | - Thomas P Sakmar
- From the Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York 10065,
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22
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Mapping the naloxone binding sites on the mu-opioid receptor using cell-based photocrosslinkers. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:336-343. [DOI: 10.1016/j.bbapap.2016.12.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 12/02/2016] [Accepted: 12/20/2016] [Indexed: 11/22/2022]
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23
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Dormán G, Nakamura H, Pulsipher A, Prestwich GD. The Life of Pi Star: Exploring the Exciting and Forbidden Worlds of the Benzophenone Photophore. Chem Rev 2016; 116:15284-15398. [PMID: 27983805 DOI: 10.1021/acs.chemrev.6b00342] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The widespread applications of benzophenone (BP) photochemistry in biological chemistry, bioorganic chemistry, and material science have been prominent in both academic and industrial research. BP photophores have unique photochemical properties: upon n-π* excitation at 365 nm, a biradicaloid triplet state is formed reversibly, which can abstract a hydrogen atom from accessible C-H bonds; the radicals subsequently recombine, creating a stable covalent C-C bond. This light-directed covalent attachment process is exploited in many different ways: (i) binding/contact site mapping of ligand (or protein)-protein interactions; (ii) identification of molecular targets and interactome mapping; (iii) proteome profiling; (iv) bioconjugation and site-directed modification of biopolymers; (v) surface grafting and immobilization. BP photochemistry also has many practical advantages, including low reactivity toward water, stability in ambient light, and the convenient excitation at 365 nm. In addition, several BP-containing building blocks and reagents are commercially available. In this review, we explore the "forbidden" (transitions) and excitation-activated world of photoinduced covalent attachment of BP photophores by touring a colorful palette of recent examples. In this exploration, we will see the pros and cons of using BP photophores, and we hope that both novice and expert photolabelers will enjoy and be inspired by the breadth and depth of possibilities.
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Affiliation(s)
- György Dormán
- Targetex llc , Dunakeszi H-2120, Hungary.,Faculty of Pharmacy, University of Szeged , Szeged H-6720, Hungary
| | - Hiroyuki Nakamura
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology , Yokohama 226-8503, Japan
| | - Abigail Pulsipher
- GlycoMira Therapeutics, Inc. , Salt Lake City, Utah 84108, United States.,Division of Head and Neck Surgery, Rhinology - Sinus and Skull Base Surgery, Department of Surgery, University of Utah School of Medicine , Salt Lake City, Utah 84108, United States
| | - Glenn D Prestwich
- Division of Head and Neck Surgery, Rhinology - Sinus and Skull Base Surgery, Department of Surgery, University of Utah School of Medicine , Salt Lake City, Utah 84108, United States
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24
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Tian H, Fürstenberg A, Huber T. Labeling and Single-Molecule Methods To Monitor G Protein-Coupled Receptor Dynamics. Chem Rev 2016; 117:186-245. [DOI: 10.1021/acs.chemrev.6b00084] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- He Tian
- Laboratory of Chemical Biology
and Signal Transduction, The Rockefeller University, 1230 York
Avenue, New York, New York 10065, United States
| | - Alexandre Fürstenberg
- Laboratory of Chemical Biology
and Signal Transduction, The Rockefeller University, 1230 York
Avenue, New York, New York 10065, United States
| | - Thomas Huber
- Laboratory of Chemical Biology
and Signal Transduction, The Rockefeller University, 1230 York
Avenue, New York, New York 10065, United States
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25
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Genetically encoded photocrosslinkers locate the high-affinity binding site of antidepressant drugs in the human serotonin transporter. Nat Commun 2016; 7:11261. [PMID: 27089947 PMCID: PMC4838859 DOI: 10.1038/ncomms11261] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 03/07/2016] [Indexed: 02/02/2023] Open
Abstract
Despite the well-established role of the human serotonin transporter (hSERT) in the treatment of depression, the molecular details of antidepressant drug binding are still not fully understood. Here we utilize amber codon suppression in a membrane-bound transporter protein to encode photocrosslinking unnatural amino acids (UAAs) into 75 different positions in hSERT. UAAs are incorporated with high specificity, and functionally active transporters have similar transport properties and pharmacological profiles compared with wild-type transporters. We employ ultraviolet-induced crosslinking with p-azido-L-phenylalanine (azF) at selected positions in hSERT to map the binding site of imipramine, a prototypical tricyclic antidepressant, and vortioxetine, a novel multimodal antidepressant. We find that the two antidepressants crosslink with azF incorporated at different positions within the central substrate-binding site of hSERT, while no crosslinking is observed at the vestibular-binding site. Taken together, our data provide direct evidence for defining the high-affinity antidepressant binding site in hSERT. Molecular details of how antidepressant drugs bind to the human serotonin transporter are not currently clear. Here, the authors introduce photo-cross-linkers into the protein and map the binding site of several antidepressants.
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26
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Kufareva I, Gustavsson M, Holden LG, Qin L, Zheng Y, Handel TM. Disulfide Trapping for Modeling and Structure Determination of Receptor: Chemokine Complexes. Methods Enzymol 2016; 570:389-420. [PMID: 26921956 DOI: 10.1016/bs.mie.2015.12.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Despite the recent breakthrough advances in GPCR crystallography, structure determination of protein-protein complexes involving chemokine receptors and their endogenous chemokine ligands remains challenging. Here, we describe disulfide trapping, a methodology for generating irreversible covalent binary protein complexes from unbound protein partners by introducing two cysteine residues, one per interaction partner, at selected positions within their interaction interface. Disulfide trapping can serve at least two distinct purposes: (i) stabilization of the complex to assist structural studies and/or (ii) determination of pairwise residue proximities to guide molecular modeling. Methods for characterization of disulfide-trapped complexes are described and evaluated in terms of throughput, sensitivity, and specificity toward the most energetically favorable crosslinks. Due to abundance of native disulfide bonds at receptor:chemokine interfaces, disulfide trapping of their complexes can be associated with intramolecular disulfide shuffling and result in misfolding of the component proteins; because of this, evidence from several experiments is typically needed to firmly establish a positive disulfide crosslink. An optimal pipeline that maximizes throughput and minimizes time and costs by early triage of unsuccessful candidate constructs is proposed.
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Affiliation(s)
- Irina Kufareva
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
| | - Martin Gustavsson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
| | - Lauren G Holden
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
| | - Ling Qin
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
| | - Yi Zheng
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
| | - Tracy M Handel
- Department of Pharmacology, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA.
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27
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Structural dynamics and energetics underlying allosteric inactivation of the cannabinoid receptor CB1. Proc Natl Acad Sci U S A 2015; 112:8469-74. [PMID: 26100912 DOI: 10.1073/pnas.1500895112] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
G protein-coupled receptors (GPCRs) are surprisingly flexible molecules that can do much more than simply turn on G proteins. Some even exhibit biased signaling, wherein the same receptor preferentially activates different G-protein or arrestin signaling pathways depending on the type of ligand bound. Why this behavior occurs is still unclear, but it can happen with both traditional ligands and ligands that bind allosterically outside the orthosteric receptor binding pocket. Here, we looked for structural mechanisms underlying these phenomena in the marijuana receptor CB1. Our work focused on the allosteric ligand Org 27569, which has an unusual effect on CB1-it simultaneously increases agonist binding, decreases G--protein activation, and induces biased signaling. Using classical pharmacological binding studies, we find that Org 27569 binds to a unique allosteric site on CB1 and show that it can act alone (without need for agonist cobinding). Through mutagenesis studies, we find that the ability of Org 27569 to bind is related to how much receptor is in an active conformation that can couple with G protein. Using these data, we estimated the energy differences between the inactive and active states. Finally, site-directed fluorescence labeling studies show the CB1 structure stabilized by Org 27569 is different and unique from that stabilized by antagonist or agonist. Specifically, transmembrane helix 6 (TM6) movements associated with G-protein activation are blocked, but at the same time, helix 8/TM7 movements are enhanced, suggesting a possible mechanism for the ability of Org 27569 to induce biased signaling.
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28
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Tyagi S, Lemke EA. Single-molecule FRET and crosslinking studies in structural biology enabled by noncanonical amino acids. Curr Opin Struct Biol 2015; 32:66-73. [DOI: 10.1016/j.sbi.2015.02.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2014] [Revised: 01/24/2015] [Accepted: 02/05/2015] [Indexed: 10/23/2022]
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29
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Wu L, Xu B. Analysis of protein ligand-receptor binding by photoaffinity cross-linking. ACTA ACUST UNITED AC 2015; 79:19.26.1-19.26.14. [PMID: 25640895 DOI: 10.1002/0471140864.ps1926s79] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Photoaffinity cross-linking is a rapidly developing technology for studying biomolecular interactions, including protein ligand-receptor binding. This technology provides detailed binding information including receptor contact sites, active conformation of receptor-ligand complexes, global binding surfaces, and binding modes. Advancements in genetic technology have enabled non-natural photoactive amino acid derivatives to be incorporated into designer or target proteins, providing a host of new opportunities for manufacturing protein photo-probes while bypassing the traditional peptide or small protein limits of classical chemical synthesis. This unit provides several protocols for performing basic photoaffinity cross-linking and related analyses for applications in ligand-receptor binding and protein-protein interactions.
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Affiliation(s)
- Ling Wu
- Department of Biochemistry and Center for Drug Discovery, Virginia Polytechnic Institute and State University, Blacksburg, Virginia
| | - Bin Xu
- Department of Biochemistry and Center for Drug Discovery, Virginia Polytechnic Institute and State University, Blacksburg, Virginia
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30
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Devaraneni PK, Martin GM, Olson EM, Zhou Q, Shyng SL. Structurally distinct ligands rescue biogenesis defects of the KATP channel complex via a converging mechanism. J Biol Chem 2015; 290:7980-91. [PMID: 25637631 DOI: 10.1074/jbc.m114.634576] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Small molecules that correct protein misfolding and misprocessing defects offer a potential therapy for numerous human diseases. However, mechanisms underlying pharmacological correction of such defects, especially in heteromeric complexes with structurally diverse constituent proteins, are not well understood. Here we investigate how two chemically distinct compounds, glibenclamide and carbamazepine, correct biogenesis defects in ATP-sensitive potassium (KATP) channels composed of sulfonylurea receptor 1 (SUR1) and Kir6.2. We present evidence that despite structural differences, carbamazepine and glibenclamide compete for binding to KATP channels, and both drugs share a binding pocket in SUR1 to exert their effects. Moreover, both compounds engage Kir6.2, in particular the distal N terminus of Kir6.2, which is involved in normal channel biogenesis, for their chaperoning effects on SUR1 mutants. Conversely, both drugs can correct channel biogenesis defects caused by Kir6.2 mutations in a SUR1-dependent manner. Using an unnatural, photocross-linkable amino acid, azidophenylalanine, genetically encoded in Kir6.2, we demonstrate in living cells that both drugs promote interactions between the distal N terminus of Kir6.2 and SUR1. These findings reveal a converging pharmacological chaperoning mechanism wherein glibenclamide and carbamazepine stabilize the heteromeric subunit interface critical for channel biogenesis to overcome defective biogenesis caused by mutations in individual subunits.
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Affiliation(s)
- Prasanna K Devaraneni
- From the Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon 97239
| | - Gregory M Martin
- From the Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon 97239
| | - Erik M Olson
- From the Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon 97239
| | - Qing Zhou
- From the Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon 97239
| | - Show-Ling Shyng
- From the Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon 97239
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31
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Scholten DJ, Wijtmans M, van Senten JR, Custers H, Stunnenberg A, de Esch IJP, Smit MJ, Leurs R. Pharmacological Characterization of [3H]VUF11211, a Novel Radiolabeled Small-Molecule Inverse Agonist for the Chemokine Receptor CXCR3. Mol Pharmacol 2015; 87:639-48. [DOI: 10.1124/mol.114.095265] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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32
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Naganathan S, Ray-Saha S, Park M, Tian H, Sakmar TP, Huber T. Multiplex detection of functional G protein-coupled receptors harboring site-specifically modified unnatural amino acids. Biochemistry 2015; 54:776-86. [PMID: 25524496 PMCID: PMC4310623 DOI: 10.1021/bi501267x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
We developed a strategy for identifying
positions in G protein-coupled
receptors that are amenable to bioorthogonal modification with a peptide
epitope tag under cell culturing conditions. We introduced the unnatural
amino acid p-azido-l-phenylalanine (azF)
into human CC chemokine receptor 5 (CCR5) at site-specific amber codon
mutations. We then used strain-promoted azide–alkyne [3+2]
cycloaddition to label the azF-CCR5 variants with a FLAG peptide epitope-conjugated
aza-dibenzocyclooctyne (DBCO) reagent. A microtiter plate-based sandwich
fluorophore-linked immunosorbent assay was used to probe simultaneously
the FLAG epitope and the receptor using infrared dye-conjugated antibodies
so that the extent of DBCO incorporation, corresponding nominally
to labeling efficiency, could be quantified ratiometrically. The extent
of incorporation of DBCO at the various sites was evaluated in the
context of a recent crystal structure of maraviroc-bound CCR5. We
observed that labeling efficiency varied dramatically depending on
the topological location of the azF in CCR5. Interestingly, position
109 in transmembrane helix 3, located in a hydrophobic cavity on the
extracellular side of the receptor, was labeled most efficiently.
Because the bioorthogonal labeling and detection strategy described
might be used to introduce a variety of different peptide epitopes
or fluorophores into engineered expressed receptors, it might prove
to be useful for a wide range of applications, including single-molecule
detection studies of receptor trafficking and signaling mechanism.
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Affiliation(s)
- Saranga Naganathan
- Laboratory of Chemical Biology & Signal Transduction, The Rockefeller University , New York, New York 10065, United States
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Abstract
Rhodopsin is a key light-sensitive protein expressed exclusively in rod photoreceptor cells of the retina. Failure to express this transmembrane protein causes a lack of rod outer segment formation and progressive retinal degeneration, including the loss of cone photoreceptor cells. Molecular studies of rhodopsin have paved the way to understanding a large family of cell-surface membrane proteins called G protein-coupled receptors (GPCRs). Work started on rhodopsin over 100 years ago still continues today with substantial progress made every year. These activities underscore the importance of rhodopsin as a prototypical GPCR and receptor required for visual perception-the fundamental process of translating light energy into a biochemical cascade of events culminating in vision.
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Affiliation(s)
- Lukas Hofmann
- Department of Pharmacology, School of Medicine, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH, 44106, USA
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34
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Schiller SM. Protein Tectons in Synthetic Biology. Synth Biol (Oxf) 2015. [DOI: 10.1007/978-3-319-02783-8_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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35
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Abstract
Experimental structure determination for G protein-coupled receptors (GPCRs) and especially their complexes with protein and peptide ligands is at its infancy. In the absence of complex structures, molecular modeling and docking play a large role not only by providing a proper 3D context for interpretation of biochemical and biophysical data, but also by prospectively guiding experiments. Experimentally confirmed restraints may help improve the accuracy and information content of the computational models. Here we present a hybrid molecular modeling protocol that integrates heterogeneous experimental data with force field-based calculations in the stochastic global optimization of the conformations and relative orientations of binding partners. Some experimental data, such as pharmacophore-like chemical fields or disulfide-trapping restraints, can be seamlessly incorporated in the protocol, while other types of data are more useful at the stage of solution filtering. The protocol was successfully applied to modeling and design of a stable construct that resulted in crystallization of the first complex between a chemokine and its receptor. Examples from this work are used to illustrate the steps of the protocol. The utility of different types of experimental data for modeling and docking is discussed and caveats associated with data misinterpretation are highlighted.
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36
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Park M, Tian H, Naganathan S, Sakmar TP, Huber T. Quantitative Multi-color Detection Strategies for Bioorthogonally Labeled GPCRs. Methods Mol Biol 2015; 1335:67-93. [PMID: 26260595 DOI: 10.1007/978-1-4939-2914-6_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We describe multiple bioorthogonal approaches to label G protein-coupled receptors (GPCRs) heterologously expressed in mammalian cells. The use of genetically encoded unnatural amino acids as bioorthogonal tags results in receptors that are expressed at lower levels than even their low abundance wild-type counterparts. Therefore, reproducible and sensitive quantification of the labeled GPCRs is extremely important and conventional methods are simply not sufficiently accurate and precise. Silver stains lack reproducibility, spectroscopic methods using fluorescent ligands are limited to quantifying only functional receptor molecules, and immunoassays using epitope tags derived from rhodopsin are particularly variable for low-abundance GPCRs. To avoid these shortcomings, we employ near infrared (NIR) imaging-based methods that enable simultaneous multi-color detection of two different antigens, thus facilitating the ratiometric analysis of bioorthogonally modified GPCRs. We anticipate that these multi-color detection strategies will provide new tools for quantitatively assessing stoichiometrically labeled GPCRs for studies of signalosomes and for structure-function relationships at a single molecule level.
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Affiliation(s)
- Minyoung Park
- Laboratory of Chemical Biology & Signal Transduction, The Rockefeller University, New York, NY, 10065, USA
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37
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Leisle L, Valiyaveetil F, Mehl RA, Ahern CA. Incorporation of Non-Canonical Amino Acids. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 869:119-51. [PMID: 26381943 DOI: 10.1007/978-1-4939-2845-3_7] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
In this chapter we discuss the strengths, caveats and technical considerations of three approaches for reprogramming the chemical composition of selected amino acids within a membrane protein. In vivo nonsense suppression in the Xenopus laevis oocyte, evolved orthogonal tRNA and aminoacyl-tRNA synthetase pairs and protein ligation for biochemical production of semisynthetic proteins have been used successfully for ion channel and receptor studies. The level of difficulty for the application of each approach ranges from trivial to technically demanding, yet all have untapped potential in their application to membrane proteins.
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Affiliation(s)
- Lilia Leisle
- Department of Molecular Physiology and Biophysics, University of Iowa, 51 Newton Road, 52246, Iowa City, IA, USA
| | - Francis Valiyaveetil
- Department of Physiology and Pharmacology, Oregon Health and Sciences University, 97239, Portland, OR, USA
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University Corvallis, 97331, Corvallis, OR, USA
| | - Christopher A Ahern
- Department of Molecular Physiology and Biophysics, University of Iowa, 51 Newton Road, 52246, Iowa City, IA, USA.
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38
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Wang W, Li T, Felsovalyi K, Chen C, Cardozo T, Krogsgaard M. Quantitative analysis of T cell receptor complex interaction sites using genetically encoded photo-cross-linkers. ACS Chem Biol 2014; 9:2165-72. [PMID: 25061810 PMCID: PMC4168801 DOI: 10.1021/cb500351s] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
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The T cell receptor (TCR)-cluster
of differentiation 3 (CD3) signaling
complex plays an important role in initiation of adaptive immune responses,
but weak interactions have obstructed delineation of the individual
TCR-CD3 subunit interactions during T cell signaling. Here, we demonstrate
that unnatural amino acids (UAA) can be used to photo-cross-link subunits
of TCR-CD3 on the cell surface. Incorporating UAA in mammalian cells
is usually a low efficiency process. In addition, TCR-CD3 is composed
of eight subunits and both TCR and CD3 chains are required for expression
on the cell surface. Photo-cross-linking of UAAs for studying protein
complexes such as TCR-CD3 is challenging due to the difficulty of
transfecting and expressing multisubunit protein complexes in cells
combined with the low efficiency of UAA incorporation. Here, we demonstrate
that by systematic optimization, we can incorporate UAA in TCR-CD3
with high efficiency. Accordingly, the incorporated UAA can be used
for site-specific photo-cross-linking experiments to pinpoint protein
interaction sites, as well as to confirm interaction sites identified
by X-ray crystallography. We systemically compared two different photo-cross-linkers—p-azido-phenylalanine
(pAzpa) and H-p-Bz-Phe-OH (pBpa)—for their ability to map protein
subunit interactions in the 2B4 TCR. pAzpa was found to have higher
cross-linking efficiency, indicating that optimization of the selection
of the most optimal cross-linker is important for correct identification
of protein–protein interactions. This method is therefore suitable
for studying interaction sites of large, dynamic heteromeric protein
complexes associated with various cellular membrane systems.
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Affiliation(s)
| | | | | | - Chunlai Chen
- Pennsylvania
Muscle Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania United States
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39
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Huber T, Sakmar T. Chemical Biology Methods for Investigating G Protein-Coupled Receptor Signaling. ACTA ACUST UNITED AC 2014; 21:1224-37. [DOI: 10.1016/j.chembiol.2014.08.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 07/21/2014] [Accepted: 08/20/2014] [Indexed: 11/26/2022]
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40
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Ligand- and mutation-induced conformational selection in the CCR5 chemokine G protein-coupled receptor. Proc Natl Acad Sci U S A 2014; 111:13040-5. [PMID: 25157173 DOI: 10.1073/pnas.1413216111] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
We predicted the structural basis for pleiotropic signaling of the C-C chemokine type 5 (CCR5) G protein-coupled receptor (GPCR) by predicting the binding of several ligands to the lower-energy conformations of the CCR5 receptor and 11 mutants. For each case, we predicted the ∼ 20 most stable conformations for the receptor along with the binding sites for four anti-HIV ligands. We found that none of the ligands bind to the lowest-energy apo-receptor conformation. The three ligands with a similar pharmacophore (Maraviroc, PF-232798, and Aplaviroc) bind to a specific higher-energy receptor conformation whereas TAK-779 (with a different pharmacophore) binds to a different high-energy conformation. This result is in agreement with the very different binding-site profiles for these ligands obtained by us and others. The predicted Maraviroc binding site agrees with the recent structure of CCR5 receptor cocrystallized with Maraviroc. We performed 11 site-directed mutagenesis experiments to validate the predicted binding sites. Here, we independently predicted the lowest 10 mutant protein conformations for each of the 11 mutants and then docked the ligands to these lowest conformations. We found the predicted binding energies to be in excellent agreement with our mutagenesis experiments. These results show that, for GPCRs, each ligand can stabilize a different protein conformation, complicating the use of cocrystallized structures for ligand screening. Moreover, these results show that a single-point mutation in a GPCR can dramatically alter the available low-energy conformations, which in turn alters the binding site, potentially altering downstream signaling events. These studies validate the conformational selection paradigm for the pleiotropic function and structural plasticity of GPCRs.
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41
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Tian H, Naganathan S, Kazmi MA, Schwartz TW, Sakmar TP, Huber T. Bioorthogonal fluorescent labeling of functional G-protein-coupled receptors. Chembiochem 2014; 15:1820-9. [PMID: 25045132 DOI: 10.1002/cbic.201402193] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Indexed: 11/12/2022]
Abstract
Novel methods are required for site-specific, quantitative fluorescent labeling of G-protein-coupled receptors (GPCRs) and other difficult-to-express membrane proteins. Ideally, fluorescent probes should perturb the native structure and function as little as possible. We evaluated bioorthogonal reactions to label genetically encoded p-acetyl-L-phenylalanine (AcF) or p-azido-L-phenylalanine (azF) residues in receptors heterologously expressed in mammalian cells. We found that keto-selective reagents were not truly bioorthogonal, possibly owing to post-translational protein oxidation reactions. In contrast, the strain-promoted [3+2] azide-alkyne cycloaddition (SpAAC) with dibenzocyclooctyne (DIBO) reagents yielded stoichiometric conjugates with azF-rhodopsin while undergoing negligible background reactions. As one application of this technique, we used Alexa488-rhodopsin to measure the kinetics of ligand uptake and release in membrane-mimetic bicelles using a novel fluorescence-quenching assay.
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Affiliation(s)
- He Tian
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, 1230 York Avenue, New York, NY 10065 (USA)
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42
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Valentin-Hansen L, Park M, Huber T, Grunbeck A, Naganathan S, Schwartz TW, Sakmar TP. Mapping substance P binding sites on the neurokinin-1 receptor using genetic incorporation of a photoreactive amino acid. J Biol Chem 2014; 289:18045-54. [PMID: 24831006 DOI: 10.1074/jbc.m113.527085] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Substance P (SP) is a neuropeptide that mediates numerous physiological responses, including transmission of pain and inflammation through the neurokinin-1 (NK1) receptor, a G protein-coupled receptor. Previous mutagenesis studies and photoaffinity labeling using ligand analogues suggested that the binding site for SP includes multiple domains in the N-terminal (Nt) segment and the second extracellular loop (ECLII) of NK1. To map precisely the NK1 residues that interact with SP, we applied a novel receptor-based targeted photocross-linking approach. We used amber codon suppression to introduce the photoreactive unnatural amino acid p-benzoyl-l-phenylalanine (BzF) at 11 selected individual positions in the Nt tail (residues 11-21) and 23 positions in the ECLII (residues 170(C-10)-193(C+13)) of NK1. The 34 NK1 variants were expressed in mammalian HEK293 cells and retained the ability to interact with a fluorescently labeled SP analog. Notably, 10 of the receptor variants with BzF in the Nt tail and 4 of those with BzF in ECLII cross-linked efficiently to SP, indicating that these 14 sites are juxtaposed to SP in the ligand-bound receptor. These results show that two distinct regions of the NK1 receptor possess multiple determinants for SP binding and demonstrate the utility of genetically encoded photocross-linking to map complex multitopic binding sites on G protein-coupled receptors in a cell-based assay format.
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Affiliation(s)
- Louise Valentin-Hansen
- From the Laboratory for Molecular Pharmacology, Department of Neuroscience and Pharmacology, University of Copenhagen, The Panum Institute, Blegdamsvej 3, 2200 Copenhagen, Denmark, Section for Metabolic Receptology and Enteroendocrinology, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark, and
| | - Minyoung Park
- Section for Metabolic Receptology and Enteroendocrinology, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark, and Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York 10065
| | - Thomas Huber
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York 10065
| | - Amy Grunbeck
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York 10065
| | - Saranga Naganathan
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York 10065
| | - Thue W Schwartz
- From the Laboratory for Molecular Pharmacology, Department of Neuroscience and Pharmacology, University of Copenhagen, The Panum Institute, Blegdamsvej 3, 2200 Copenhagen, Denmark, Section for Metabolic Receptology and Enteroendocrinology, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark, and
| | - Thomas P Sakmar
- Section for Metabolic Receptology and Enteroendocrinology, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark, and Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York 10065
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43
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Modeling the allosteric modulation of CCR5 function by Maraviroc. DRUG DISCOVERY TODAY. TECHNOLOGIES 2014; 10:e297-305. [PMID: 24050281 DOI: 10.1016/j.ddtec.2012.07.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Maraviroc is a non-peptidic, low molecular weight CC chemokine receptor 5 (CCR5) ligand that has recently been marketed for the treatment of HIV infected individuals. This review discusses recent molecular modeling studies of CCR5 by homology to CXC chemokine receptor 4, their contribution to the understanding of the allosteric mode of action of the inhibitor and their potential for the development of future drugs with improved efficiency and preservation of CCR5 biological functions.
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44
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Preston GW, Radford SE, Ashcroft AE, Wilson AJ. Analysis of amyloid nanostructures using photo-cross-linking: in situ comparison of three widely used photo-cross-linkers. ACS Chem Biol 2014; 9:761-8. [PMID: 24372480 PMCID: PMC3964826 DOI: 10.1021/cb400731s] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Photoinduced cross-linking (PIC) has become a powerful tool in chemical biology for the identification and mapping of stable or transient interactions between biomacromolecules and their (unknown) ligands. However, the value of PIC for in vitro and in vivo structural proteomics can be realized only if cross-linking reports accurately on biomacromolecule secondary, tertiary, and quaternary structures with residue-specific resolution. Progress in this area requires rigorous and comparative studies of PIC reagents, but despite widespread use of PIC, these have rarely been performed. The use of PIC to report reliably on noncovalent structure is therefore limited, and its potentials have yet to be fully realized. In the present study, we compared the abilities of three probes, phenyl trifluoromethyldiazirine (TFMD), benzophenone (BP), and phenylazide (PA), to record structural information within a biomolecular complex. For this purpose, we employed a self-assembled amyloid-like peptide nanostructure as a tightly and specifically packed model environment in which to photolyze the reagents. Information about PIC products was gathered using mass spectrometry and ion mobility spectrometry, and the data were interpreted using a mechanism-oriented approach. While all three PIC groups appeared to generate information within the packed peptide environment, the data highlight technical limitations of BP and PA. On the other hand, TFMD displayed accuracy and generated straightforward results. Thus TFMD, with its robust and rapid photochemistry, was shown to be an ideal probe for cross-linking of peptide nanostructures. The implications of our findings for detailed analyses of complex systems, including those that are transiently populated, are discussed.
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Affiliation(s)
- George W. Preston
- School
of Chemistry, ‡Astbury Centre for Structural Molecular Biology, and §School of Molecular and Cellular Biology,
Faculty of Biological Sciences, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, United Kingdom
| | - Sheena E. Radford
- School
of Chemistry, ‡Astbury Centre for Structural Molecular Biology, and §School of Molecular and Cellular Biology,
Faculty of Biological Sciences, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, United Kingdom
| | - Alison. E. Ashcroft
- School
of Chemistry, ‡Astbury Centre for Structural Molecular Biology, and §School of Molecular and Cellular Biology,
Faculty of Biological Sciences, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, United Kingdom
| | - Andrew J. Wilson
- School
of Chemistry, ‡Astbury Centre for Structural Molecular Biology, and §School of Molecular and Cellular Biology,
Faculty of Biological Sciences, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, United Kingdom
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45
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Ray-Saha S, Huber T, Sakmar TP. Antibody epitopes on g protein-coupled receptors mapped with genetically encoded photoactivatable cross-linkers. Biochemistry 2014; 53:1302-10. [PMID: 24490954 PMCID: PMC3985944 DOI: 10.1021/bi401289p] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
![]()
We
developed a strategy for creating epitope maps of monoclonal
antibodies (mAbs) that bind to G protein-coupled receptors (GPCRs)
containing photo-cross-linkers. Using human CXC chemokine receptor
4 (CXCR4) as a model system, we genetically incorporated the photolabile
unnatural amino acid p-azido-l-phenylalanine
(azF) at various positions within extracellular loop 2 (EC2). We then
mapped the interactions of the azF-CXCR4 variants with mAb 12G5 using
targeted loss-of-function studies and photo-cross-linking in whole
cells in a microplate-based format. We used a novel variation of a
whole cell enzyme-linked immunosorbent assay to quantitate cross-linking
efficiency. 12G5 cross-linked primarily to residues 184, 178, and
189 in EC2 of CXCR4. Mapping of the data to the crystal structure
of CXCR4 showed a distinct mAb epitope footprint with the photo-cross-linked
residues clustered around the loss-of-function sites. We also used
the targeted photo-cross-linking approach to study the interaction
of human CC chemokine receptor 5 (CCR5) with PRO 140, a humanized
mAb that inhibits human immunodeficiency virus-1 cellular entry, and
2D7. The mAbs produced distinct cross-linking patterns on EC2 of CCR5.
PRO 140 cross-linked primarily to residues 174 and 175 at the amino-terminal
end of EC2, and 2D7 cross-linked mainly to residues 170, 176, and
184. These results were mapped to the recent crystal structure of
CCR5 in complex with maraviroc, showing cross-linked residues at the
tip of the maraviroc binding crevice formed by EC2. As a strategy
for mapping mAb epitopes on GPCRs, our targeted photo-cross-linking
method is complementary to loss-of-function mutagenesis results and
should be especially useful for studying mAbs with discontinuous epitopes.
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Affiliation(s)
- Sarmistha Ray-Saha
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University , 1230 York Avenue, New York, New York 10065, United States
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46
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Tracy CM, Gray AJ, Cuéllar J, Shaw TS, Howlett AC, Taylor RM, Prince JT, Ahn NG, Valpuesta JM, Willardson BM. Programmed cell death protein 5 interacts with the cytosolic chaperonin containing tailless complex polypeptide 1 (CCT) to regulate β-tubulin folding. J Biol Chem 2013; 289:4490-502. [PMID: 24375412 DOI: 10.1074/jbc.m113.542159] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Programmed cell death protein 5 (PDCD5) has been proposed to act as a pro-apoptotic factor and tumor suppressor. However, the mechanisms underlying its apoptotic function are largely unknown. A proteomics search for binding partners of phosducin-like protein, a co-chaperone for the cytosolic chaperonin containing tailless complex polypeptide 1 (CCT), revealed a robust interaction between PDCD5 and CCT. PDCD5 formed a complex with CCT and β-tubulin, a key CCT-folding substrate, and specifically inhibited β-tubulin folding. Cryo-electron microscopy studies of the PDCD5·CCT complex suggested a possible mechanism of inhibition of β-tubulin folding. PDCD5 bound the apical domain of the CCTβ subunit, projecting above the folding cavity without entering it. Like PDCD5, β-tubulin also interacts with the CCTβ apical domain, but a second site is found at the sensor loop deep within the folding cavity. These orientations of PDCD5 and β-tubulin suggest that PDCD5 sterically interferes with β-tubulin binding to the CCTβ apical domain and inhibits β-tubulin folding. Given the importance of tubulins in cell division and proliferation, PDCD5 might exert its apoptotic function at least in part through inhibition of β-tubulin folding.
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Affiliation(s)
- Christopher M Tracy
- From the Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602
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47
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48
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SuperBiHelix method for predicting the pleiotropic ensemble of G-protein-coupled receptor conformations. Proc Natl Acad Sci U S A 2013; 111:E72-8. [PMID: 24344284 DOI: 10.1073/pnas.1321233111] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
There is overwhelming evidence that G-protein-coupled receptors (GPCRs) exhibit several distinct low-energy conformations, each of which might favor binding to different ligands and/or lead to different downstream functions. Understanding the function of such proteins requires knowledge of the ensemble of low-energy configurations that might play a role in this pleiotropic functionality. We earlier reported the BiHelix method for efficiently sampling the (12)(7) = 35 million conformations resulting from 30° rotations about the axis (η) of all seven transmembrane helices (TMHs), showing that the experimental structure is reliably selected as the best conformation from this ensemble. However, various GPCRs differ sufficiently in the tilts of the TMHs that this method need not predict the optimum conformation starting from any other template. In this paper, we introduce the SuperBiHelix method in which the tilt angles (θ, ϕ) are optimized simultaneously with rotations (η) efficiently enough that it is practical and sufficient to sample (5 × 3 × 5)(7) = 13 trillion configurations. This method can correctly identify the optimum structure of a GPCR starting with the template from a different GPCR. We have validated this method by predicting known crystal structure conformations starting from the template of a different protein structure. We find that the SuperBiHelix conformational ensemble includes the higher energy conformations associated with the active protein in addition to those associated with the more stable inactive protein. This methodology was then applied to design and experimentally confirm structures of three mutants of the CB1 cannabinoid receptor associated with different functions.
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Coin I, Katritch V, Sun T, Xiang Z, Siu FY, Beyermann M, Stevens RC, Wang L. Genetically encoded chemical probes in cells reveal the binding path of urocortin-I to CRF class B GPCR. Cell 2013; 155:1258-69. [PMID: 24290358 DOI: 10.1016/j.cell.2013.11.008] [Citation(s) in RCA: 139] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 08/26/2013] [Accepted: 11/07/2013] [Indexed: 01/19/2023]
Abstract
Molecular determinants regulating the activation of class B G-protein-coupled receptors (GPCRs) by native peptide agonists are largely unknown. We have investigated here the interaction between the corticotropin releasing factor receptor type 1 (CRF1R) and its native 40-mer peptide ligand Urocortin-I directly in mammalian cells. By incorporating unnatural amino acid photochemical and new click-chemical probes into the intact receptor expressed in the native membrane of live cells, 44 intermolecular spatial constraints have been derived for the ligand-receptor interaction. The data were analyzed in the context of the recently resolved crystal structure of CRF1R transmembrane domain and existing extracellular domain structures, yielding a complete conformational model for the peptide-receptor complex. Structural features of the receptor-ligand complex yield molecular insights on the mechanism of receptor activation and the basis for discrimination between agonist and antagonist function.
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Affiliation(s)
- Irene Coin
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
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Grunbeck A, Sakmar TP. Probing G Protein-Coupled Receptor—Ligand Interactions with Targeted Photoactivatable Cross-Linkers. Biochemistry 2013; 52:8625-32. [DOI: 10.1021/bi401300y] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Amy Grunbeck
- Laboratory of Chemical Biology
and Signal Transduction, The Rockefeller University, 1230 York
Avenue, New York, New
York 10065, United States
| | - Thomas P. Sakmar
- Laboratory of Chemical Biology
and Signal Transduction, The Rockefeller University, 1230 York
Avenue, New York, New
York 10065, United States
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