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Tzortzini E, Kolocouris A. Molecular Biophysics of Class A G Protein Coupled Receptors-Lipids Interactome at a Glance-Highlights from the A 2A Adenosine Receptor. Biomolecules 2023; 13:957. [PMID: 37371538 DOI: 10.3390/biom13060957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/25/2023] [Accepted: 05/28/2023] [Indexed: 06/29/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are embedded in phospholipid membrane bilayers with cholesterol representing 34% of the total lipid content in mammalian plasma membranes. Membrane lipids interact with GPCRs structures and modulate their function and drug-stimulated signaling through conformational selection. It has been shown that anionic phospholipids form strong interactions between positively charged residues in the G protein and the TM5-TM6-TM 7 cytoplasmic interface of class A GPCRs stabilizing the signaling GPCR-G complex. Cholesterol with a high content in plasma membranes can be identified in more specific sites in the transmembrane region of GPCRs, such as the Cholesterol Consensus Motif (CCM) and Cholesterol Recognition Amino Acid Consensus (CRAC) motifs and other receptor dependent and receptor state dependent sites. Experimental biophysical methods, atomistic (AA) MD simulations and coarse-grained (CG) molecular dynamics simulations have been applied to investigate these interactions. We emphasized here the impact of phosphatidyl inositol-4,5-bisphosphate (PtdIns(4,5)P2 or PIP2), a minor phospholipid component and of cholesterol on the function-related conformational equilibria of the human A2A adenosine receptor (A2AR), a representative receptor in class A GPCR. Several GPCRs of class A interacted with PIP2 and cholesterol and in many cases the mechanism of the modulation of their function remains unknown. This review provides a helpful comprehensive overview for biophysics that enter the field of GPCRs-lipid systems.
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Affiliation(s)
- Efpraxia Tzortzini
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, 15771 Athens, Greece
| | - Antonios Kolocouris
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, 15771 Athens, Greece
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Tzortzini E, Corey RA, Kolocouris A. Comparative Study of Receptor-, Receptor State-, and Membrane-Dependent Cholesterol Binding Sites in A 2A and A 1 Adenosine Receptors Using Coarse-Grained Molecular Dynamics Simulations. J Chem Inf Model 2023; 63:928-949. [PMID: 36637988 DOI: 10.1021/acs.jcim.2c01181] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
We used coarse-grained molecular dynamics (CG MD) simulations to study protein-cholesterol interactions for different activation states of the A2A adenosine receptor (A2AR) and the A1 adenosine receptor (A1R) and predict new cholesterol binding sites indicating amino acid residues with a high residence time in three biologically relevant membranes. Compared to 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)-cholesterol and POPC-phosphatidylinositol-bisphosphate (PIP2)-cholesterol, the plasma mimetic membrane best described the cholesterol binding sites previously detected for the inactive state of A2AR and revealed the binding sites with long-lasting amino acid residues. We observed that using the plasma mimetic membrane and plotting residues with cholesterol residence time ≥2 μs, our CG MD simulations captured most obviously the cholesterol-protein interactions. For the inactive A2AR, we identified one more binding site in which cholesterol is bound to residues with a long residence time compared to the previously detected, for the active A1R, three binding sites, and for the inactive A1R, two binding sites. We calculated that for the active states, cholesterol binds to residues with a much longer residence time compared to the inactive state for both A2AR and A1R. The stability of the identified binding sites to A1R or A2AR with CG MD simulations was additionally investigated with potential of mean force calculations using umbrella sampling. We observed that the binding sites with residues to which cholesterol has a long residence time in A2AR have shallow binding free energy minima compared to the related binding sites in A1R, suggesting a stronger binding for cholesterol to A1R. The differences in binding sites in which cholesterol is stabilized and interacts with residues with a long residence time between active and inactive states of A1R and A2AR can be important for differences in functional activity and orthosteric agonist or antagonist affinity and can be used for the design of allosteric modulators, which can bind through lipid pathways. We observed a stronger binding for cholesterol to A1R (i.e., generally higher association rates) compared to A2AR, which remains to be demonstrated. For the active states, cholesterol binds to residues with much longer residence times compared to the inactive state for both A2AR and A1R. Taken together, binding sites of active A1R may be considered as promising allosteric targets.
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Affiliation(s)
- Efpraxia Tzortzini
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771Athens, Greece
| | - Robin A Corey
- Department of Biochemistry, University of Oxford, OxfordOX1 3QU, United Kingdom
| | - Antonios Kolocouris
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771Athens, Greece
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3
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Cui W, Dong J, Wang S, Vogel H, Zou R, Yuan S. Molecular basis of ligand selectivity for melatonin receptors. RSC Adv 2023; 13:4422-4430. [PMID: 36760312 PMCID: PMC9891099 DOI: 10.1039/d2ra06693a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 01/20/2023] [Indexed: 02/04/2023] Open
Abstract
Sleep disorders in adults are related to adverse health effects such as reduced quality of life and increased mortality. About 30-40% of adults are suffering from different sleep disorders. The human melatonin receptors (MT1 and MT2) are family A G protein-coupled receptors that respond to the neurohormone melatonin MEL which regulates circadian rhythm and sleep. Many efforts have been made to develop drugs targeting melatonin receptors to treat insomnia, circadian rhythm disorders, and even cancer. However, designing subtype-selective melatonergic drugs remains challenging due to their high similarities in both sequences and structures. MEL (a function-selective compound with a bulky β-naphthyl group) behaves as an MT2-selective antagonist, whereas it is an agonist of MT1. Here, molecular dynamics simulations were used to investigate the ligand selectivity of MT receptors at the atomic level. We found that the binding conformation of MEL differs in different melatonin receptors. In MT1, the naphthalene ring of MEL forms a structure perpendicular to the membrane surface. In contrast, there is a 130° angle between the naphthalene ring of MEL and the membrane surface in MT2. Because of this conformational difference, the MEL leads to a constant water channel in MT1 which activates the receptor. However, MEL hinders the formation of continuous water channels, resulting in an inactive state of MT2. Furthermore, we found that A1173.29 in MT2 is a crucial amino acid capable of hindering the conformational flip of the MEL molecule. These results, coupled with previous functional data, reveal that although MT1 and MT2 share highly similar orthosteric ligand-binding pockets, they also display distinctive features that could be used to design selective compounds. Our findings provide new insights into functionally selective melatonergic drug development for sleep disorders.
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Affiliation(s)
- Wenqiang Cui
- The Research Center for Computer-aided Drug Discovery, Institute of Biomedicine and Biotechnology, The Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences Shenzhen 518055 China .,University of Chinese Academy of Sciences Beijing 100049 China
| | - Junlin Dong
- The Research Center for Computer-aided Drug Discovery, Institute of Biomedicine and Biotechnology, The Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences Shenzhen 518055 China .,University of Chinese Academy of Sciences Beijing 100049 China
| | - Shiyu Wang
- The Research Center for Computer-aided Drug Discovery, Institute of Biomedicine and Biotechnology, The Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences Shenzhen 518055 China .,University of Chinese Academy of Sciences Beijing 100049 China
| | - Horst Vogel
- The Research Center for Computer-aided Drug Discovery, Institute of Biomedicine and Biotechnology, The Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences Shenzhen 518055 China
| | - Rongfeng Zou
- The Research Center for Computer-aided Drug Discovery, Institute of Biomedicine and Biotechnology, The Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences Shenzhen 518055 China
| | - Shuguang Yuan
- The Research Center for Computer-aided Drug Discovery, Institute of Biomedicine and Biotechnology, The Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences Shenzhen 518055 China
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Spinaci A, Buccioni M, Catarzi D, Cui C, Colotta V, Dal Ben D, Cescon E, Francucci B, Grieco I, Lambertucci C, Marucci G, Bassani D, Pavan M, Varano F, Federico S, Spalluto G, Moro S, Volpini R. "Dual Anta-Inhibitors" of the A 2A Adenosine Receptor and Casein Kinase CK1delta: Synthesis, Biological Evaluation, and Molecular Modeling Studies. Pharmaceuticals (Basel) 2023; 16:167. [PMID: 37259317 PMCID: PMC9960553 DOI: 10.3390/ph16020167] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/13/2023] [Accepted: 01/18/2023] [Indexed: 08/13/2023] Open
Abstract
Based on a screening of a chemical library of A2A adenosine receptor (AR) antagonists, a series of di- and tri-substituted adenine derivatives were synthesized and tested for their ability to inhibit the activity of the enzyme casein kinase 1 delta (CK1δ) and to bind adenosine receptors (ARs). Some derivatives, here called "dual anta-inhibitors", demonstrated good CK1δ inhibitory activity combined with a high binding affinity, especially for the A2AAR. The N6-methyl-(2-benzimidazolyl)-2-dimethyamino-9-cyclopentyladenine (17, IC50 = 0.59 μM and KiA2A = 0.076 μM) showed the best balance of A2AAR affinity and CK1δ inhibitory activity. Computational studies were performed to simulate, at the molecular level, the protein-ligand interactions involving the compounds of our series. Hence, the dual anta-inhibitor 17 could be considered the lead compound of new therapeutic agents endowed with synergistic effects for the treatment of chronic neurodegenerative and cancer diseases.
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Affiliation(s)
- Andrea Spinaci
- Medicinal Chemistry Unit, School of Pharmacy, University of Camerino, Via Madonna delle Carceri, 62032 Camerino, Italy
| | - Michela Buccioni
- Medicinal Chemistry Unit, School of Pharmacy, University of Camerino, Via Madonna delle Carceri, 62032 Camerino, Italy
| | - Daniela Catarzi
- Area del Farmaco e Salute del Bambino, Sezione di Farmaceutica e Nutraceutica, Dipartimento di Neuroscienze, Psicologia, Università degli Studi di Firenze, Via Ugo Schiff, 6, Sesto Fiorentino, 50019 Florence, Italy
| | - Chang Cui
- Medicinal Chemistry Unit, School of Pharmacy, University of Camerino, Via Madonna delle Carceri, 62032 Camerino, Italy
| | - Vittoria Colotta
- Area del Farmaco e Salute del Bambino, Sezione di Farmaceutica e Nutraceutica, Dipartimento di Neuroscienze, Psicologia, Università degli Studi di Firenze, Via Ugo Schiff, 6, Sesto Fiorentino, 50019 Florence, Italy
| | - Diego Dal Ben
- Medicinal Chemistry Unit, School of Pharmacy, University of Camerino, Via Madonna delle Carceri, 62032 Camerino, Italy
| | - Eleonora Cescon
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via Licio Giorgieri 1, 34127 Trieste, Italy
| | - Beatrice Francucci
- Medicinal Chemistry Unit, School of Pharmacy, University of Camerino, Via Madonna delle Carceri, 62032 Camerino, Italy
| | - Ilenia Grieco
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via Licio Giorgieri 1, 34127 Trieste, Italy
| | - Catia Lambertucci
- Medicinal Chemistry Unit, School of Pharmacy, University of Camerino, Via Madonna delle Carceri, 62032 Camerino, Italy
| | - Gabriella Marucci
- Medicinal Chemistry Unit, School of Pharmacy, University of Camerino, Via Madonna delle Carceri, 62032 Camerino, Italy
| | - Davide Bassani
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, 35131 Padova, Italy
| | - Matteo Pavan
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, 35131 Padova, Italy
| | - Flavia Varano
- Area del Farmaco e Salute del Bambino, Sezione di Farmaceutica e Nutraceutica, Dipartimento di Neuroscienze, Psicologia, Università degli Studi di Firenze, Via Ugo Schiff, 6, Sesto Fiorentino, 50019 Florence, Italy
| | - Stephanie Federico
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via Licio Giorgieri 1, 34127 Trieste, Italy
| | - Giampiero Spalluto
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via Licio Giorgieri 1, 34127 Trieste, Italy
| | - Stefano Moro
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, 35131 Padova, Italy
| | - Rosaria Volpini
- Medicinal Chemistry Unit, School of Pharmacy, University of Camerino, Via Madonna delle Carceri, 62032 Camerino, Italy
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Han R, Yoon H, Yoo J, Lee Y. Systematic analyses of the sequence conservation and ligand interaction patterns of purinergic P1 and P2Y receptors provide a structural basis for receptor selectivity. Comput Struct Biotechnol J 2023; 21:889-898. [PMID: 36698973 PMCID: PMC9860165 DOI: 10.1016/j.csbj.2023.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/09/2023] [Accepted: 01/09/2023] [Indexed: 01/11/2023] Open
Abstract
Purinergic receptors are membrane proteins that regulate numerous cellular functions by catalyzing reactions involving purine nucleotides or nucleosides. Among the three receptor families, i.e., P1, P2X, and P2Y, the P1 and P2Y receptors share common structural features of class A GPCR. Comprehensive sequence and structural analysis revealed that the P1 and P2Y receptors belong to two distinct groups. They exhibit different ligand-binding site features that can distinguish between specific activators. These specific amino acid residues in the binding cavity may be involved in the selectivity and unique pharmacological behavior of each subtype. In this study, we conducted a structure-based analysis of purinergic P1 and P2Y receptors to identify their evolutionary signature and obtain structural insights into ligand recognition and selectivity. The structural features of the P1 and P2Y receptor classes were compared based on sequence conservation and ligand interaction patterns. Orthologous protein sequences were collected for the P1 and P2Y receptors, and sequence conservation was calculated based on Shannon entropy to identify highly conserved residues. To analyze the ligand interaction patterns, we performed docking studies on the P1 and P2Y receptors using known ligand information extracted from the ChEMBL database. We analyzed how the conserved residues are related to ligand-binding sites and how the key interacting residues differ between P1 and P2Y receptors, or between agonists and antagonists. We extracted new similarities and differences between the receptor subtypes, and the results can be used for designing new ligands by predicting hotspot residues that are important for functional selectivity.
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Dmitrieva DA, Kotova TV, Safronova NA, Sadova AA, Dashevskii DE, Mishin AV. Protein Design Strategies for the Structural–Functional Studies of G Protein-Coupled Receptors. BIOCHEMISTRY (MOSCOW) 2023; 88:S192-S226. [PMID: 37069121 DOI: 10.1134/s0006297923140110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
G protein-coupled receptors (GPCRs) are an important family of membrane proteins responsible for many physiological functions in human body. High resolution GPCR structures are required to understand their molecular mechanisms and perform rational drug design, as GPCRs play a crucial role in a variety of diseases. That is difficult to obtain for the wild-type proteins because of their low stability. In this review, we discuss how this problem can be solved by using protein design strategies developed to obtain homogeneous stabilized GPCR samples for crystallization and cryoelectron microscopy.
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Affiliation(s)
- Daria A Dmitrieva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Tatiana V Kotova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Nadezda A Safronova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Alexandra A Sadova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Dmitrii E Dashevskii
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Alexey V Mishin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.
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7
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Dalton KM, Greisman JB, Hekstra DR. A unifying Bayesian framework for merging X-ray diffraction data. Nat Commun 2022; 13:7764. [PMID: 36522310 PMCID: PMC9755530 DOI: 10.1038/s41467-022-35280-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 11/22/2022] [Indexed: 12/23/2022] Open
Abstract
Novel X-ray methods are transforming the study of the functional dynamics of biomolecules. Key to this revolution is detection of often subtle conformational changes from diffraction data. Diffraction data contain patterns of bright spots known as reflections. To compute the electron density of a molecule, the intensity of each reflection must be estimated, and redundant observations reduced to consensus intensities. Systematic effects, however, lead to the measurement of equivalent reflections on different scales, corrupting observation of changes in electron density. Here, we present a modern Bayesian solution to this problem, which uses deep learning and variational inference to simultaneously rescale and merge reflection observations. We successfully apply this method to monochromatic and polychromatic single-crystal diffraction data, as well as serial femtosecond crystallography data. We find that this approach is applicable to the analysis of many types of diffraction experiments, while accurately and sensitively detecting subtle dynamics and anomalous scattering.
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Affiliation(s)
- Kevin M Dalton
- Department of Molecular & Cellular Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Jack B Greisman
- Department of Molecular & Cellular Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Doeke R Hekstra
- Department of Molecular & Cellular Biology, Harvard University, Cambridge, MA, 02138, USA.
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA.
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Barends TR, Stauch B, Cherezov V, Schlichting I. Serial femtosecond crystallography. NATURE REVIEWS. METHODS PRIMERS 2022; 2:59. [PMID: 36643971 PMCID: PMC9833121 DOI: 10.1038/s43586-022-00141-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
With the advent of X-ray Free Electron Lasers (XFELs), new, high-throughput serial crystallography techniques for macromolecular structure determination have emerged. Serial femtosecond crystallography (SFX) and related methods provide possibilities beyond canonical, single-crystal rotation crystallography by mitigating radiation damage and allowing time-resolved studies with unprecedented temporal resolution. This primer aims to assist structural biology groups with little or no experience in serial crystallography planning and carrying out a successful SFX experiment. It discusses the background of serial crystallography and its possibilities. Microcrystal growth and characterization methods are discussed, alongside techniques for sample delivery and data processing. Moreover, it gives practical tips for preparing an experiment, what to consider and do during a beamtime and how to conduct the final data analysis. Finally, the Primer looks at various applications of SFX, including structure determination of membrane proteins, investigation of radiation damage-prone systems and time-resolved studies.
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Affiliation(s)
- Thomas R.M. Barends
- Department for Biological Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Benjamin Stauch
- Department of Chemistry, The Bridge Institute, University of Southern California, Los Angeles, CA, USA
| | - Vadim Cherezov
- Department of Chemistry, The Bridge Institute, University of Southern California, Los Angeles, CA, USA
| | - Ilme Schlichting
- Department for Biological Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany,
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9
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Wang X, Yuan S, Chan HCS. Translocation Mechanism of Allosteric Sodium Ions in β 2-Adrenoceptor. J Chem Inf Model 2022; 62:3090-3095. [PMID: 35695388 DOI: 10.1021/acs.jcim.2c00170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The allosteric modulation of G-protein-coupled receptors (GPCRs) by sodium ions has received significant attention as the crystal structures of several receptors show the binding of sodium ions (Na+) at the conserved D2.50. Theoretical studies have shown that extracellular Na+ would enter the allosteric D2.50 via the orthosteric site. However, it remains unclear how the bound allosteric Na+ would leave the GPCRs. In this study, we performed molecular dynamics (MD) simulations to illustrate the energy barriers of Na+ transfer through the transmembrane helix bundle of β2AR. In contrast to the postulations from other GPCRs, the translocation of this allosteric Na+ into the intracellular side is found to be significantly difficult. Hence, the translocation direction could be receptor-specific.
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Affiliation(s)
- Xueying Wang
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Shuguang Yuan
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,Alpha Mol Science Ltd, Shenzhen 518055, China
| | - H C Stephen Chan
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
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McGraw C, Koretz KS, Oseid D, Lyman E, Robinson AS. Cholesterol Dependent Activity of the Adenosine A 2A Receptor Is Modulated via the Cholesterol Consensus Motif. Molecules 2022; 27:molecules27113529. [PMID: 35684466 PMCID: PMC9182133 DOI: 10.3390/molecules27113529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/22/2022] [Accepted: 05/23/2022] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Membrane cholesterol dysregulation has been shown to alter the activity of the adenosine A2A receptor (A2AR), a G protein-coupled receptor, thereby implicating cholesterol levels in diseases such as Alzheimer's and Parkinson's. A limited number of A2AR crystal structures show the receptor interacting with cholesterol, as such molecular simulations are often used to predict cholesterol interaction sites. METHODS Here, we use experimental methods to determine whether a specific interaction between amino acid side chains in the cholesterol consensus motif (CCM) of full length, wild-type human A2AR, and cholesterol modulates activity of the receptor by testing the effects of mutational changes on functional consequences, including ligand binding, G protein coupling, and downstream activation of cyclic AMP. RESULTS AND CONCLUSIONS Our data, taken with previously published studies, support a model of receptor state-dependent binding between cholesterol and the CCM, whereby cholesterol facilitates both G protein coupling and downstream signaling of A2AR.
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Affiliation(s)
- Claire McGraw
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, LA 70118, USA; (C.M.); (D.O.)
| | - Kirsten Swonger Koretz
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA;
| | - Daniel Oseid
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, LA 70118, USA; (C.M.); (D.O.)
| | - Edward Lyman
- Department of Physics and Astronomy, University of Delaware, Newark, DE 19711, USA;
| | - Anne Skaja Robinson
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA;
- Correspondence: ; Tel.: +1-(412)-268-7673
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11
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Mahmood A, Iqbal J. Purinergic receptors modulators: An emerging pharmacological tool for disease management. Med Res Rev 2022; 42:1661-1703. [PMID: 35561109 DOI: 10.1002/med.21888] [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: 12/08/2021] [Revised: 03/16/2022] [Accepted: 05/04/2022] [Indexed: 11/10/2022]
Abstract
Purinergic signaling is mediated through extracellular nucleotides (adenosine 5'-triphosphate, uridine-5'-triphosphate, adenosine diphosphate, uridine-5'-diphosphate, and adenosine) that serve as signaling molecules. In the early 1990s, purines and pyrimidine receptors were cloned and characterized drawing the attention of scientists toward this aspect of cellular signaling. This signaling pathway is comprised of four subtypes of adenosine receptors (P1), eight subtypes of G-coupled protein receptors (P2YRs), and seven subtypes of ligand-gated ionotropic receptors (P2XRs). In current studies, the pathophysiology and therapeutic potentials of these receptors have been focused on. Various ligands, modulating the functions of purinergic receptors, are in current clinical practices for the treatment of various neurodegenerative disorders and cardiovascular diseases. Moreover, several purinergic receptors ligands are in advanced phases of clinical trials as a remedy for depression, epilepsy, autism, osteoporosis, atherosclerosis, myocardial infarction, diabetes, irritable bowel syndrome, and cancers. In the present study, agonists and antagonists of purinergic receptors have been summarized that may serve as pharmacological tools for drug design and development.
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Affiliation(s)
- Abid Mahmood
- Centre for Advanced Drug Research, COMSATS University Islamabad, Abbottabad, Pakistan
| | - Jamshed Iqbal
- Centre for Advanced Drug Research, COMSATS University Islamabad, Abbottabad, Pakistan
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12
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IJzerman AP, Jacobson KA, Müller CE, Cronstein BN, Cunha RA. International Union of Basic and Clinical Pharmacology. CXII: Adenosine Receptors: A Further Update. Pharmacol Rev 2022; 74:340-372. [PMID: 35302044 PMCID: PMC8973513 DOI: 10.1124/pharmrev.121.000445] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Our previous International Union of Basic and Clinical Pharmacology report on the nomenclature and classification of adenosine receptors (2011) contained a number of emerging developments with respect to this G protein-coupled receptor subfamily, including protein structure, protein oligomerization, protein diversity, and allosteric modulation by small molecules. Since then, a wealth of new data and results has been added, allowing us to explore novel concepts such as target binding kinetics and biased signaling of adenosine receptors, to examine a multitude of receptor structures and novel ligands, to gauge new pharmacology, and to evaluate clinical trials with adenosine receptor ligands. This review should therefore be considered a further update of our previous reports from 2001 and 2011. SIGNIFICANCE STATEMENT: Adenosine receptors (ARs) are of continuing interest for future treatment of chronic and acute disease conditions, including inflammatory diseases, neurodegenerative afflictions, and cancer. The design of AR agonists ("biased" or not) and antagonists is largely structure based now, thanks to the tremendous progress in AR structural biology. The A2A- and A2BAR appear to modulate the immune response in tumor biology. Many clinical trials for this indication are ongoing, whereas an A2AAR antagonist (istradefylline) has been approved as an anti-Parkinson agent.
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Affiliation(s)
- Adriaan P IJzerman
- Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands (A.P.IJ.); National Institutes of Health, National Institute of Diabetes and Digestive and Kidney Diseases, Molecular Recognition Section, Bethesda, Maryland (K.A.J.); Universität Bonn, Bonn, Germany (C.E.M.); New York University School of Medicine, New York, New York (B.N.C.); and Center for Neurosciences and Cell Biology and Faculty of Medicine, University of Coimbra, Coimbra, Portugal (R.A.C.)
| | - Kenneth A Jacobson
- Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands (A.P.IJ.); National Institutes of Health, National Institute of Diabetes and Digestive and Kidney Diseases, Molecular Recognition Section, Bethesda, Maryland (K.A.J.); Universität Bonn, Bonn, Germany (C.E.M.); New York University School of Medicine, New York, New York (B.N.C.); and Center for Neurosciences and Cell Biology and Faculty of Medicine, University of Coimbra, Coimbra, Portugal (R.A.C.)
| | - Christa E Müller
- Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands (A.P.IJ.); National Institutes of Health, National Institute of Diabetes and Digestive and Kidney Diseases, Molecular Recognition Section, Bethesda, Maryland (K.A.J.); Universität Bonn, Bonn, Germany (C.E.M.); New York University School of Medicine, New York, New York (B.N.C.); and Center for Neurosciences and Cell Biology and Faculty of Medicine, University of Coimbra, Coimbra, Portugal (R.A.C.)
| | - Bruce N Cronstein
- Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands (A.P.IJ.); National Institutes of Health, National Institute of Diabetes and Digestive and Kidney Diseases, Molecular Recognition Section, Bethesda, Maryland (K.A.J.); Universität Bonn, Bonn, Germany (C.E.M.); New York University School of Medicine, New York, New York (B.N.C.); and Center for Neurosciences and Cell Biology and Faculty of Medicine, University of Coimbra, Coimbra, Portugal (R.A.C.)
| | - Rodrigo A Cunha
- Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands (A.P.IJ.); National Institutes of Health, National Institute of Diabetes and Digestive and Kidney Diseases, Molecular Recognition Section, Bethesda, Maryland (K.A.J.); Universität Bonn, Bonn, Germany (C.E.M.); New York University School of Medicine, New York, New York (B.N.C.); and Center for Neurosciences and Cell Biology and Faculty of Medicine, University of Coimbra, Coimbra, Portugal (R.A.C.)
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13
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Wang J, Bhattarai A, Do HN, Akhter S, Miao Y. Molecular Simulations and Drug Discovery of Adenosine Receptors. Molecules 2022; 27:2054. [PMID: 35408454 PMCID: PMC9000248 DOI: 10.3390/molecules27072054] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/18/2022] [Accepted: 03/20/2022] [Indexed: 02/02/2023] Open
Abstract
G protein-coupled receptors (GPCRs) represent the largest family of human membrane proteins. Four subtypes of adenosine receptors (ARs), the A1AR, A2AAR, A2BAR and A3AR, each with a unique pharmacological profile and distribution within the tissues in the human body, mediate many physiological functions and serve as critical drug targets for treating numerous human diseases including cancer, neuropathic pain, cardiac ischemia, stroke and diabetes. The A1AR and A3AR preferentially couple to the Gi/o proteins, while the A2AAR and A2BAR prefer coupling to the Gs proteins. Adenosine receptors were the first subclass of GPCRs that had experimental structures determined in complex with distinct G proteins. Here, we will review recent studies in molecular simulations and computer-aided drug discovery of the adenosine receptors and also highlight their future research opportunities.
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Affiliation(s)
| | | | | | | | - Yinglong Miao
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66047, USA; (J.W.); (A.B.); (H.N.D.); (S.A.)
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14
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Clabbers MTB, Shiriaeva A, Gonen T. MicroED: conception, practice and future opportunities. IUCRJ 2022; 9:169-179. [PMID: 35371502 PMCID: PMC8895021 DOI: 10.1107/s2052252521013063] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 12/08/2021] [Indexed: 06/14/2023]
Abstract
This article documents a keynote seminar presented at the IUCr Congress in Prague, 2021. The cryo-EM method microcrystal electron diffraction is described and put in the context of macromolecular electron crystallography from its origins in 2D crystals of membrane proteins to today's application to 3D crystals a millionth the size of that needed for X-ray crystallography. Milestones in method development and applications are described with an outlook to the future.
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Affiliation(s)
- Max T. B. Clabbers
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095, USA
| | - Anna Shiriaeva
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095, USA
| | - Tamir Gonen
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095, USA
- Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095, USA
- Department of Physiology, University of California, Los Angeles, CA 90095, USA
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15
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Studying membrane proteins with MicroED. Biochem Soc Trans 2022; 50:231-239. [PMID: 35191473 PMCID: PMC9022970 DOI: 10.1042/bst20210911] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 01/26/2022] [Accepted: 01/28/2022] [Indexed: 12/27/2022]
Abstract
The structural investigation of biological macromolecules is indispensable in understanding the molecular mechanisms underlying diseases. Several structural biology techniques have been introduced to unravel the structural facets of biomolecules. Among these, the electron cryomicroscopy (cryo-EM) method microcrystal electron diffraction (MicroED) has produced atomic resolution structures of important biological and small molecules. Since its inception in 2013, MicroED established a demonstrated ability for solving structures of difficult samples using vanishingly small crystals. However, membrane proteins remain the next big frontier for MicroED. The intrinsic properties of membrane proteins necessitate improved sample handling and imaging techniques to be developed and optimized for MicroED. Here, we summarize the milestones of electron crystallography of two-dimensional crystals leading to MicroED of three-dimensional crystals. Then, we focus on four different membrane protein families and discuss representatives from each family solved by MicroED.
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16
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Pan D, Oyama R, Sato T, Nakane T, Mizunuma R, Matsuoka K, Joti Y, Tono K, Nango E, Iwata S, Nakatsu T, Kato H. Crystal structure of CmABCB1 multi-drug exporter in lipidic mesophase revealed by LCP-SFX. IUCRJ 2022; 9:134-145. [PMID: 35059217 PMCID: PMC8733880 DOI: 10.1107/s2052252521011611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 11/03/2021] [Indexed: 06/14/2023]
Abstract
CmABCB1 is a Cyanidioschyzon merolae homolog of human ABCB1, a well known ATP-binding cassette (ABC) transporter responsible for multi-drug resistance in various cancers. Three-dimensional structures of ABCB1 homologs have revealed the snapshots of inward- and outward-facing states of the transporters in action. However, sufficient information to establish the sequential movements of the open-close cycles of the alternating-access model is still lacking. Serial femtosecond crystallography (SFX) using X-ray free-electron lasers has proven its worth in determining novel structures and recording sequential conformational changes of proteins at room temperature, especially for medically important membrane proteins, but it has never been applied to ABC transporters. In this study, 7.7 mono-acyl-glycerol with cholesterol as the host lipid was used and obtained well diffracting microcrystals of the 130 kDa CmABCB1 dimer. Successful SFX experiments were performed by adjusting the viscosity of the crystal suspension of the sponge phase with hy-droxy-propyl methyl-cellulose and using the high-viscosity sample injector for data collection at the SACLA beamline. An outward-facing structure of CmABCB1 at a maximum resolution of 2.22 Å is reported, determined by SFX experiments with crystals formed in the lipidic cubic phase (LCP-SFX), which has never been applied to ABC transporters. In the type I crystal, CmABCB1 dimers interact with adjacent molecules via not only the nucleotide-binding domains but also the transmembrane domains (TMDs); such an interaction was not observed in the previous type II crystal. Although most parts of the structure are similar to those in the previous type II structure, the substrate-exit region of the TMD adopts a different configuration in the type I structure. This difference between the two types of structures reflects the flexibility of the substrate-exit region of CmABCB1, which might be essential for the smooth release of various substrates from the transporter.
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Affiliation(s)
- Dongqing Pan
- Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Ryo Oyama
- Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Tomomi Sato
- Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Takanori Nakane
- Department of Biological Science, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ryo Mizunuma
- Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Keita Matsuoka
- Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yasumasa Joti
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Eriko Nango
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - So Iwata
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Toru Nakatsu
- Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Hiroaki Kato
- Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
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17
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Nass K, Bacellar C, Cirelli C, Dworkowski F, Gevorkov Y, James D, Johnson PJM, Kekilli D, Knopp G, Martiel I, Ozerov D, Tolstikova A, Vera L, Weinert T, Yefanov O, Standfuss J, Reiche S, Milne CJ. Pink-beam serial femtosecond crystallography for accurate structure-factor determination at an X-ray free-electron laser. IUCRJ 2021; 8:905-920. [PMID: 34804544 PMCID: PMC8562661 DOI: 10.1107/s2052252521008046] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 08/05/2021] [Indexed: 05/25/2023]
Abstract
Serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs) enables essentially radiation-damage-free macromolecular structure determination using microcrystals that are too small for synchrotron studies. However, SFX experiments often require large amounts of sample in order to collect highly redundant data where some of the many stochastic errors can be averaged out to determine accurate structure-factor amplitudes. In this work, the capability of the Swiss X-ray free-electron laser (SwissFEL) was used to generate large-bandwidth X-ray pulses [Δλ/λ = 2.2% full width at half-maximum (FWHM)], which were applied in SFX with the aim of improving the partiality of Bragg spots and thus decreasing sample consumption while maintaining the data quality. Sensitive data-quality indicators such as anomalous signal from native thaumatin micro-crystals and de novo phasing results were used to quantify the benefits of using pink X-ray pulses to obtain accurate structure-factor amplitudes. Compared with data measured using the same setup but using X-ray pulses with typical quasi-monochromatic XFEL bandwidth (Δλ/λ = 0.17% FWHM), up to fourfold reduction in the number of indexed diffraction patterns required to obtain similar data quality was achieved. This novel approach, pink-beam SFX, facilitates the yet underutilized de novo structure determination of challenging proteins at XFELs, thereby opening the door to more scientific breakthroughs.
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Affiliation(s)
- Karol Nass
- Paul Scherrer Institut, Forschungstrasse 111, Villigen 5232, Switzerland
| | - Camila Bacellar
- Paul Scherrer Institut, Forschungstrasse 111, Villigen 5232, Switzerland
| | - Claudio Cirelli
- Paul Scherrer Institut, Forschungstrasse 111, Villigen 5232, Switzerland
| | - Florian Dworkowski
- Paul Scherrer Institut, Forschungstrasse 111, Villigen 5232, Switzerland
| | - Yaroslav Gevorkov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Daniel James
- Paul Scherrer Institut, Forschungstrasse 111, Villigen 5232, Switzerland
| | | | - Demet Kekilli
- Paul Scherrer Institut, Forschungstrasse 111, Villigen 5232, Switzerland
| | - Gregor Knopp
- Paul Scherrer Institut, Forschungstrasse 111, Villigen 5232, Switzerland
| | - Isabelle Martiel
- Paul Scherrer Institut, Forschungstrasse 111, Villigen 5232, Switzerland
| | - Dmitry Ozerov
- Paul Scherrer Institut, Forschungstrasse 111, Villigen 5232, Switzerland
| | - Alexandra Tolstikova
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Laura Vera
- Paul Scherrer Institut, Forschungstrasse 111, Villigen 5232, Switzerland
| | - Tobias Weinert
- Paul Scherrer Institut, Forschungstrasse 111, Villigen 5232, Switzerland
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Jörg Standfuss
- Paul Scherrer Institut, Forschungstrasse 111, Villigen 5232, Switzerland
| | - Sven Reiche
- Paul Scherrer Institut, Forschungstrasse 111, Villigen 5232, Switzerland
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18
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Heavy Atom Detergent/Lipid Combined X-ray Crystallography for Elucidating the Structure-Function Relationships of Membrane Proteins. MEMBRANES 2021; 11:membranes11110823. [PMID: 34832053 PMCID: PMC8625833 DOI: 10.3390/membranes11110823] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/22/2021] [Accepted: 10/23/2021] [Indexed: 02/03/2023]
Abstract
Membrane proteins reside in the lipid bilayer of biomembranes and the structure and function of these proteins are closely related to their interactions with lipid molecules. Structural analyses of interactions between membrane proteins and lipids or detergents that constitute biological or artificial model membranes are important for understanding the functions and physicochemical properties of membrane proteins and biomembranes. Determination of membrane protein structures is much more difficult when compared with that of soluble proteins, but the development of various new technologies has accelerated the elucidation of the structure-function relationship of membrane proteins. This review summarizes the development of heavy atom derivative detergents and lipids that can be used for structural analysis of membrane proteins and their interactions with detergents/lipids, including their application with X-ray free-electron laser crystallography.
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19
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Martynowycz MW, Shiriaeva A, Ge X, Hattne J, Nannenga BL, Cherezov V, Gonen T. MicroED structure of the human adenosine receptor determined from a single nanocrystal in LCP. Proc Natl Acad Sci U S A 2021; 118:e2106041118. [PMID: 34462357 PMCID: PMC8433539 DOI: 10.1073/pnas.2106041118] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
G protein-coupled receptors (GPCRs), or seven-transmembrane receptors, are a superfamily of membrane proteins that are critically important to physiological processes in the human body. Determining high-resolution structures of GPCRs without bound cognate signaling partners, such as a G protein, requires crystallization in lipidic cubic phase (LCP). GPCR crystals grown in LCP are often too small for traditional X-ray crystallography. These microcrystals are ideal for investigation by microcrystal electron diffraction (MicroED), but the gel-like nature of LCP makes traditional approaches to MicroED sample preparation insurmountable. Here, we show that the structure of a human A2A adenosine receptor can be determined by MicroED after converting the LCP into the sponge phase followed by focused ion-beam milling. We determined the structure of the A2A adenosine receptor to 2.8-Å resolution and resolved an antagonist in its orthosteric ligand-binding site, as well as four cholesterol molecules bound around the receptor. This study lays the groundwork for future structural studies of lipid-embedded membrane proteins by MicroED using single microcrystals that would be impossible with other crystallographic methods.
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Affiliation(s)
- Michael W Martynowycz
- HHMI, University of California, Los Angeles, CA 90095
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095
| | - Anna Shiriaeva
- Bridge Institute, University of Southern California Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA 90007
- Department of Chemistry, University of Southern California, Los Angeles, CA 90007
| | - Xuanrui Ge
- Bridge Institute, University of Southern California Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA 90007
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA 90007
| | - Johan Hattne
- HHMI, University of California, Los Angeles, CA 90095
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095
| | - Brent L Nannenga
- Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, AZ 85287
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287
| | - Vadim Cherezov
- Bridge Institute, University of Southern California Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA 90007;
- Department of Chemistry, University of Southern California, Los Angeles, CA 90007
| | - Tamir Gonen
- HHMI, University of California, Los Angeles, CA 90095;
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095
- Department of Physiology, University of California, Los Angeles, CA 90095
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20
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Zou R, Wang X, Li S, Chan HCS, Vogel H, Yuan S. The role of metal ions in G protein‐coupled receptor signalling and drug discovery. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1565] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Rongfeng Zou
- Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen China
- AlphaMol Science Ltd Shenzhen China
| | - Xueying Wang
- Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen China
| | - Shu Li
- Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen China
| | - H. C. Stephen Chan
- Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen China
| | - Horst Vogel
- Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen China
- AlphaMol Science Ltd Shenzhen China
- Ecole Polytechnique Fédérale de Lausanne (EPFL) Lausanne Switzerland
| | - Shuguang Yuan
- Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen China
- AlphaMol Science Ltd Shenzhen China
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21
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Salmaso V, Jain S, Jacobson KA. Purinergic GPCR transmembrane residues involved in ligand recognition and dimerization. Methods Cell Biol 2021; 166:133-159. [PMID: 34752329 PMCID: PMC8620127 DOI: 10.1016/bs.mcb.2021.06.001] [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] [Indexed: 09/25/2023]
Abstract
We compare the GPCR-ligand interactions and highlight important residues for recognition in purinergic receptors-from both X-ray crystallographic and cryo-EM structures. These include A1 and A2A adenosine receptors, and P2Y1 and P2Y12 receptors that respond to ADP and other nucleotides. These receptors are important drug discovery targets for immune, metabolic and nervous system disorders. In most cases, orthosteric ligands are represented, except for one allosteric P2Y1 antagonist. This review catalogs the residues and regions that engage in contacts with ligands or with other GPCR protomers in dimeric forms. Residues that are in proximity to bound ligands within purinergic GPCR families are correlated. There is extensive conservation of recognition motifs between adenosine receptors, but the P2Y1 and P2Y12 receptors are each structurally distinct in their ligand recognition. Identifying common interaction features for ligand recognition within a receptor class that has multiple structures available can aid in the drug discovery process.
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Affiliation(s)
- Veronica Salmaso
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Shanu Jain
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Kenneth A Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States.
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22
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Gorel A, Schlichting I, Barends TRM. Discerning best practices in XFEL-based biological crystallography - standards for nonstandard experiments. IUCRJ 2021; 8:532-543. [PMID: 34258002 PMCID: PMC8256713 DOI: 10.1107/s205225252100467x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 05/03/2021] [Indexed: 06/13/2023]
Abstract
Serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs) is a novel tool in structural biology. In contrast to conventional crystallography, SFX relies on merging partial intensities acquired with X-ray beams of often randomly fluctuating properties from a very large number of still diffraction images of generally randomly oriented microcrystals. For this reason, and possibly due to limitations of the still evolving data-analysis programs, XFEL-derived SFX data are typically of a lower quality than 'standard' crystallographic data. In contrast with this, the studies performed at XFELs often aim to investigate issues that require precise high-resolution data, for example to determine structures of intermediates at low occupancy, which often display very small conformational changes. This is a potentially dangerous combination and underscores the need for a critical evaluation of procedures including data-quality standards in XFEL-based structural biology. Here, such concerns are addressed.
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Affiliation(s)
- Alexander Gorel
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstr. 29, Heidelberg, 69120, Germany
| | - Ilme Schlichting
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstr. 29, Heidelberg, 69120, Germany
| | - Thomas R. M. Barends
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstr. 29, Heidelberg, 69120, Germany
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23
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Clabbers MTB, Holmes S, Muusse TW, Vajjhala PR, Thygesen SJ, Malde AK, Hunter DJB, Croll TI, Flueckiger L, Nanson JD, Rahaman MH, Aquila A, Hunter MS, Liang M, Yoon CH, Zhao J, Zatsepin NA, Abbey B, Sierecki E, Gambin Y, Stacey KJ, Darmanin C, Kobe B, Xu H, Ve T. MyD88 TIR domain higher-order assembly interactions revealed by microcrystal electron diffraction and serial femtosecond crystallography. Nat Commun 2021; 12:2578. [PMID: 33972532 PMCID: PMC8110528 DOI: 10.1038/s41467-021-22590-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 03/18/2021] [Indexed: 02/03/2023] Open
Abstract
MyD88 and MAL are Toll-like receptor (TLR) adaptors that signal to induce pro-inflammatory cytokine production. We previously observed that the TIR domain of MAL (MALTIR) forms filaments in vitro and induces formation of crystalline higher-order assemblies of the MyD88 TIR domain (MyD88TIR). These crystals are too small for conventional X-ray crystallography, but are ideally suited to structure determination by microcrystal electron diffraction (MicroED) and serial femtosecond crystallography (SFX). Here, we present MicroED and SFX structures of the MyD88TIR assembly, which reveal a two-stranded higher-order assembly arrangement of TIR domains analogous to that seen previously for MALTIR. We demonstrate via mutagenesis that the MyD88TIR assembly interfaces are critical for TLR4 signaling in vivo, and we show that MAL promotes unidirectional assembly of MyD88TIR. Collectively, our studies provide structural and mechanistic insight into TLR signal transduction and allow a direct comparison of the MicroED and SFX techniques.
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Affiliation(s)
- Max T B Clabbers
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, California, USA
| | - Susannah Holmes
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Timothy W Muusse
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Parimala R Vajjhala
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Sara J Thygesen
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Alpeshkumar K Malde
- Institute for Glycomics, Griffith University, Southport, Queensland, Australia
| | - Dominic J B Hunter
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- EMBL Australia Node in Single Molecule Science, University of New South Wales, Kensington, New South Wales, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Tristan I Croll
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Leonie Flueckiger
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Jeffrey D Nanson
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Md Habibur Rahaman
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Andrew Aquila
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Mark S Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Mengning Liang
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Chun Hong Yoon
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Jingjing Zhao
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden
| | - Nadia A Zatsepin
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Brian Abbey
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Emma Sierecki
- EMBL Australia Node in Single Molecule Science, University of New South Wales, Kensington, New South Wales, Australia
| | - Yann Gambin
- EMBL Australia Node in Single Molecule Science, University of New South Wales, Kensington, New South Wales, Australia
| | - Katryn J Stacey
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Connie Darmanin
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia.
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia.
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia.
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia.
| | - Hongyi Xu
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden.
| | - Thomas Ve
- Institute for Glycomics, Griffith University, Southport, Queensland, Australia.
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Do HN, Akhter S, Miao Y. Pathways and Mechanism of Caffeine Binding to Human Adenosine A 2A Receptor. Front Mol Biosci 2021; 8:673170. [PMID: 33987207 PMCID: PMC8111288 DOI: 10.3389/fmolb.2021.673170] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 03/24/2021] [Indexed: 11/13/2022] Open
Abstract
Caffeine (CFF) is a common antagonist to the four subtypes of adenosine G-protein-coupled receptors (GPCRs), which are critical drug targets for treating heart failure, cancer, and neurological diseases. However, the pathways and mechanism of CFF binding to the target receptors remain unclear. In this study, we have performed all-atom-enhanced sampling simulations using a robust Gaussian-accelerated molecular dynamics (GaMD) method to elucidate the binding mechanism of CFF to human adenosine A2A receptor (A2AAR). Multiple 500–1,000 ns GaMD simulations captured both binding and dissociation of CFF in the A2AAR. The GaMD-predicted binding poses of CFF were highly consistent with the x-ray crystal conformations with a characteristic hydrogen bond formed between CFF and residue N6.55 in the receptor. In addition, a low-energy intermediate binding conformation was revealed for CFF at the receptor extracellular mouth between ECL2 and TM1. While the ligand-binding pathways of the A2AAR were found similar to those of other class A GPCRs identified from previous studies, the ECL2 with high sequence divergence serves as an attractive target site for designing allosteric modulators as selective drugs of the A2AAR.
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Affiliation(s)
- Hung N Do
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS, United States
| | - Sana Akhter
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS, United States
| | - Yinglong Miao
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS, United States
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25
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The Specificity of Downstream Signaling for A 1 and A 2AR Does Not Depend on the C-Terminus, Despite the Importance of This Domain in Downstream Signaling Strength. Biomedicines 2020; 8:biomedicines8120603. [PMID: 33322210 PMCID: PMC7764039 DOI: 10.3390/biomedicines8120603] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/07/2020] [Accepted: 12/09/2020] [Indexed: 11/17/2022] Open
Abstract
Recent efforts to determine the high-resolution crystal structures for the adenosine receptors (A1R and A2AR) have utilized modifications to the native receptors in order to facilitate receptor crystallization and structure determination. One common modification is a truncation of the unstructured C-terminus, which has been utilized for all the adenosine receptor crystal structures obtained to date. Ligand binding for this truncated receptor has been shown to be similar to full-length receptor for A2AR. However, the C-terminus has been identified as a location for protein-protein interactions that may be critical for the physiological function of these important drug targets. We show that variants with A2AR C-terminal truncations lacked cAMP-linked signaling compared to the full-length receptor constructs transfected into mammalian cells (HEK-293). In addition, we show that in a humanized yeast system, the absence of the full-length C-terminus affected downstream signaling using a yeast MAPK response-based fluorescence assay, though full-length receptors showed native-like G-protein coupling. To further study the G protein coupling, we used this humanized yeast platform to explore coupling to human-yeast G-protein chimeras in a cellular context. Although the C-terminus was essential for Gα protein-associated signaling, chimeras of A1R with a C-terminus of A2AR coupled to the A1R-specific Gα (i.e., Gαi1 versus Gαs). This surprising result suggests that the C-terminus is important in the signaling strength, but not specificity, of the Gα protein interaction. This result has further implications in drug discovery, both in enabling the experimental use of chimeras for ligand design, and in the cautious interpretation of structure-based drug design using truncated receptors.
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26
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Wang Y, Yu Z, Xiao W, Lu S, Zhang J. Allosteric binding sites at the receptor-lipid bilayer interface: novel targets for GPCR drug discovery. Drug Discov Today 2020; 26:690-703. [PMID: 33301977 DOI: 10.1016/j.drudis.2020.12.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/19/2020] [Accepted: 12/01/2020] [Indexed: 01/01/2023]
Abstract
As a superfamily of membrane receptors, G-protein-coupled receptors (GPCRs) have significant roles in human physiological processes, including cell proliferation, metabolism, and neuromodulation. GPCRs are vital targets of therapeutic drugs, and their allosteric regulation represents a novel direction for drug discovery. Given the numerous breakthroughs in structural biology, diverse allosteric sites on GPCRs have been identified within the extracellular and intracellular loops, and the seven core transmembrane helices. However, a unique type of allosteric site has also been discovered at the interface of the receptor-lipid bilayer, similar to the β2-adrenergic receptor. Here, we review recent identifications of these allosteric sites and the detailed modulator-target interactions within the interface for each modulator to highlight the role of lipids in GPCR allosteric drug discovery.
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Affiliation(s)
- Ying Wang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, 200025, China
| | - Zhengtian Yu
- Nutshell Biotechnology Co., Ltd., Shanghai, China
| | - Wen Xiao
- Nutshell Biotechnology Co., Ltd., Shanghai, China
| | - Shaoyong Lu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, 200025, China; Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China.
| | - Jian Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, 200025, China; Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China.
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27
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Membrane protein crystallography in the era of modern structural biology. Biochem Soc Trans 2020; 48:2505-2524. [DOI: 10.1042/bst20200066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 02/07/2023]
Abstract
The aim of structural biology has been always the study of biological macromolecules structures and their mechanistic behaviour at molecular level. To achieve its goal, multiple biophysical methods and approaches have become part of the structural biology toolbox. Considered as one of the pillars of structural biology, X-ray crystallography has been the most successful method for solving three-dimensional protein structures at atomic level to date. It is however limited by the success in obtaining well-ordered protein crystals that diffract at high resolution. This is especially true for challenging targets such as membrane proteins (MPs). Understanding structure-function relationships of MPs at the biochemical level is vital for medicine and drug discovery as they play critical roles in many cellular processes. Though difficult, structure determination of MPs by X-ray crystallography has significantly improved in the last two decades, mainly due to many relevant technological and methodological developments. Today, numerous MP crystal structures have been solved, revealing many of their mechanisms of action. Yet the field of structural biology has also been through significant technological breakthroughs in recent years, particularly in the fields of single particle electron microscopy (cryo-EM) and X-ray free electron lasers (XFELs). Here we summarise the most important advancements in the field of MP crystallography and the significance of these developments in the present era of modern structural biology.
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Salmaso V, Jacobson KA. Purinergic Signaling: Impact of GPCR Structures on Rational Drug Design. ChemMedChem 2020; 15:1958-1973. [PMID: 32803849 PMCID: PMC8276773 DOI: 10.1002/cmdc.202000465] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Indexed: 12/16/2022]
Abstract
The purinergic signaling system includes membrane-bound receptors for extracellular purines and pyrimidines, and enzymes/transporters that regulate receptor activation by endogenous agonists. Receptors include: adenosine (A1 , A2A , A2B, and A3 ) and P2Y (P2Y1 , P2Y2 , P2Y4 , P2Y6 , P2Y11 , P2Y12 , P2Y13 , and P2Y14 ) receptors (all GPCRs), as well as P2X receptors (ion channels). Receptor activation, especially accompanying physiological stress or damage, creates a temporal sequence of signaling to counteract this stress and either mobilize (P2Rs) or suppress (ARs) immune responses. Thus, modulation of this large signaling family has broad potential for treating chronic diseases. Experimentally determined structures represent each of the three receptor families. We focus on selective purinergic agonists (A1 , A3 ), antagonists (A3 , P2Y14 ), and allosteric modulators (P2Y1 , A3 ). Examples of applying structure-based design, including the rational modification of known ligands, are presented for antithrombotic P2Y1 R antagonists and anti-inflammatory P2Y14 R antagonists and A3 AR agonists. A3 AR agonists are a potential, nonaddictive treatment for chronic neuropathic pain.
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Affiliation(s)
- Veronica Salmaso
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes & Digestive & Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kenneth A Jacobson
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes & Digestive & Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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29
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Zhu L, Chen X, Abola EE, Jing L, Liu W. Serial Crystallography for Structure-Based Drug Discovery. Trends Pharmacol Sci 2020; 41:830-839. [PMID: 32950259 PMCID: PMC7572805 DOI: 10.1016/j.tips.2020.08.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 07/17/2020] [Accepted: 08/25/2020] [Indexed: 02/07/2023]
Abstract
Rational drug discovery has greatly accelerated the development of safer and more efficacious therapeutics, assisted significantly by insights from experimentally determined 3D structures of ligands in complex with their targets. Serial crystallography (SX) with X-ray free-electron lasers has enabled structural determination using micrometer- or nanometer-size crystals. This technology, applied in the past decade to solve structures of notoriously difficult-to-study drug targets at room temperature, has now been adapted for use in synchrotron radiation facilities. Ultrashort time scales allow time-resolved characterization of dynamic structural changes and pave the road to study the molecular mechanisms by 'molecular movie.' This article summarizes the latest progress in SX technology and deliberates its demanding applications in future structure-based drug discovery.
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Affiliation(s)
- Lan Zhu
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Xiaoyu Chen
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Enrique E Abola
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Liang Jing
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Wei Liu
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA.
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30
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Nass K, Cheng R, Vera L, Mozzanica A, Redford S, Ozerov D, Basu S, James D, Knopp G, Cirelli C, Martiel I, Casadei C, Weinert T, Nogly P, Skopintsev P, Usov I, Leonarski F, Geng T, Rappas M, Doré AS, Cooke R, Nasrollahi Shirazi S, Dworkowski F, Sharpe M, Olieric N, Bacellar C, Bohinc R, Steinmetz MO, Schertler G, Abela R, Patthey L, Schmitt B, Hennig M, Standfuss J, Wang M, Milne CJ. Advances in long-wavelength native phasing at X-ray free-electron lasers. IUCRJ 2020; 7:965-975. [PMID: 33209311 PMCID: PMC7642782 DOI: 10.1107/s2052252520011379] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 08/19/2020] [Indexed: 05/31/2023]
Abstract
Long-wavelength pulses from the Swiss X-ray free-electron laser (XFEL) have been used for de novo protein structure determination by native single-wavelength anomalous diffraction (native-SAD) phasing of serial femtosecond crystallography (SFX) data. In this work, sensitive anomalous data-quality indicators and model proteins were used to quantify improvements in native-SAD at XFELs such as utilization of longer wavelengths, careful experimental geometry optimization, and better post-refinement and partiality correction. Compared with studies using shorter wavelengths at other XFELs and older software versions, up to one order of magnitude reduction in the required number of indexed images for native-SAD was achieved, hence lowering sample consumption and beam-time requirements significantly. Improved data quality and higher anomalous signal facilitate so-far underutilized de novo structure determination of challenging proteins at XFELs. Improvements presented in this work can be used in other types of SFX experiments that require accurate measurements of weak signals, for example time-resolved studies.
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Affiliation(s)
- Karol Nass
- Photon Science Division, Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, 5232, Switzerland
| | - Robert Cheng
- LeadXpro AG, Park InnovAARE, Villigen, 5234, Switzerland
| | - Laura Vera
- Photon Science Division, Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, 5232, Switzerland
| | - Aldo Mozzanica
- Photon Science Division, Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, 5232, Switzerland
| | - Sophie Redford
- Photon Science Division, Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, 5232, Switzerland
| | - Dmitry Ozerov
- Science IT, Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, 5232, Switzerland
| | - Shibom Basu
- Photon Science Division, Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, 5232, Switzerland
| | - Daniel James
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, 5232, Switzerland
| | - Gregor Knopp
- Photon Science Division, Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, 5232, Switzerland
| | - Claudio Cirelli
- Photon Science Division, Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, 5232, Switzerland
| | - Isabelle Martiel
- Photon Science Division, Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, 5232, Switzerland
| | - Cecilia Casadei
- Photon Science Division, Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, 5232, Switzerland
| | - Tobias Weinert
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, 5232, Switzerland
| | - Przemyslaw Nogly
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, Wolfgang-Pauli-Strasse 27, Zürich, 8093, Switzerland
| | - Petr Skopintsev
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, 5232, Switzerland
- Department of Biology, ETH Zürich, Wolfgang-Pauli-Strasse 27, Zürich, 8093, Switzerland
| | - Ivan Usov
- Science IT, Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, 5232, Switzerland
| | - Filip Leonarski
- Photon Science Division, Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, 5232, Switzerland
| | - Tian Geng
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG, United Kingdom
| | - Mathieu Rappas
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG, United Kingdom
| | - Andrew S. Doré
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG, United Kingdom
| | - Robert Cooke
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG, United Kingdom
| | | | - Florian Dworkowski
- Photon Science Division, Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, 5232, Switzerland
| | - May Sharpe
- Photon Science Division, Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, 5232, Switzerland
| | - Natacha Olieric
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, 5232, Switzerland
| | - Camila Bacellar
- Photon Science Division, Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, 5232, Switzerland
| | - Rok Bohinc
- Photon Science Division, Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, 5232, Switzerland
| | - Michel O. Steinmetz
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, 5232, Switzerland
- Biozentrum, University of Basel, Basel, 4056, Switzerland
| | - Gebhard Schertler
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, 5232, Switzerland
- Department of Biology, ETH Zürich, Wolfgang-Pauli-Strasse 27, Zürich, 8093, Switzerland
| | - Rafael Abela
- LeadXpro AG, Park InnovAARE, Villigen, 5234, Switzerland
| | - Luc Patthey
- Photon Science Division, Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, 5232, Switzerland
| | - Bernd Schmitt
- Photon Science Division, Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, 5232, Switzerland
| | - Michael Hennig
- LeadXpro AG, Park InnovAARE, Villigen, 5234, Switzerland
| | - Jörg Standfuss
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, 5232, Switzerland
| | - Meitian Wang
- Photon Science Division, Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, 5232, Switzerland
| | - Christopher J. Milne
- Photon Science Division, Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, 5232, Switzerland
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Lee MY, Geiger J, Ishchenko A, Han GW, Barty A, White TA, Gati C, Batyuk A, Hunter MS, Aquila A, Boutet S, Weierstall U, Cherezov V, Liu W. Harnessing the power of an X-ray laser for serial crystallography of membrane proteins crystallized in lipidic cubic phase. IUCRJ 2020; 7:976-984. [PMID: 33209312 PMCID: PMC7642783 DOI: 10.1107/s2052252520012701] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 09/17/2020] [Indexed: 05/31/2023]
Abstract
Serial femtosecond crystallography (SFX) with X-ray free-electron lasers (XFELs) has proven highly successful for structure determination of challenging membrane proteins crystallized in lipidic cubic phase; however, like most techniques, it has limitations. Here we attempt to address some of these limitations related to the use of a vacuum chamber and the need for attenuation of the XFEL beam, in order to further improve the efficiency of this method. Using an optimized SFX experimental setup in a helium atmosphere, the room-temperature structure of the adenosine A2A receptor (A2AAR) at 2.0 Å resolution is determined and compared with previous A2AAR structures determined in vacuum and/or at cryogenic temperatures. Specifically, the capability of utilizing high XFEL beam transmissions is demonstrated, in conjunction with a high dynamic range detector, to collect high-resolution SFX data while reducing crystalline material consumption and shortening the collection time required for a complete dataset. The experimental setup presented herein can be applied to future SFX applications for protein nanocrystal samples to aid in structure-based discovery efforts of therapeutic targets that are difficult to crystallize.
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Affiliation(s)
- Ming-Yue Lee
- Center for Applied Structural Discovery at the Biodesign Institute, Arizona State University, Tempe, AZ 85287-1604, USA
| | - James Geiger
- Center for Applied Structural Discovery at the Biodesign Institute, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Andrii Ishchenko
- Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, 1002 W. Childs Way, Los Angeles, CA 90089, USA
| | - Gye Won Han
- Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, 1002 W. Childs Way, Los Angeles, CA 90089, USA
| | - Anton Barty
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Thomas A White
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Cornelius Gati
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Alexander Batyuk
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Mark S Hunter
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Andrew Aquila
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Sébastien Boutet
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Uwe Weierstall
- Center for Applied Structural Discovery at the Biodesign Institute, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Vadim Cherezov
- Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, 1002 W. Childs Way, Los Angeles, CA 90089, USA
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Wei Liu
- Center for Applied Structural Discovery at the Biodesign Institute, Arizona State University, Tempe, AZ 85287-1604, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
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Cheng QD, Chung HY, Schubert R, Chia SH, Falke S, Mudogo CN, Kärtner FX, Chang G, Betzel C. Protein-crystal detection with a compact multimodal multiphoton microscope. Commun Biol 2020; 3:569. [PMID: 33051587 PMCID: PMC7553921 DOI: 10.1038/s42003-020-01275-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 09/01/2020] [Indexed: 11/28/2022] Open
Abstract
There is an increasing demand for rapid, effective methods to identify and detect protein micro- and nano-crystal suspensions for serial diffraction data collection at X-ray free-electron lasers or high-intensity micro-focus synchrotron radiation sources. Here, we demonstrate a compact multimodal, multiphoton microscope, driven by a fiber-based ultrafast laser, enabling excitation wavelengths at 775 nm and 1300 nm for nonlinear optical imaging, which simultaneously records second-harmonic generation, third-harmonic generation and three-photon excited ultraviolet fluorescence to identify and detect protein crystals with high sensitivity. The instrument serves as a valuable and important tool supporting sample scoring and sample optimization in biomolecular crystallography, which we hope will increase the capabilities and productivity of serial diffraction data collection in the future.
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Affiliation(s)
- Qing-di Cheng
- Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Building 22a Notkestrasse 85, 22607, Hamburg, Germany
| | - Hsiang-Yu Chung
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany
- Physics Department, University of Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Robin Schubert
- Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Building 22a Notkestrasse 85, 22607, Hamburg, Germany
- XFEL Biological Infrastructure Laboratory at the European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Shih-Hsuan Chia
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany
- Physics Department, University of Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Sven Falke
- Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Building 22a Notkestrasse 85, 22607, Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, University of Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Celestin Nzanzu Mudogo
- Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Building 22a Notkestrasse 85, 22607, Hamburg, Germany
| | - Franz X Kärtner
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany.
- Physics Department, University of Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.
- The Hamburg Centre for Ultrafast Imaging, University of Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.
| | - Guoqing Chang
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany.
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China.
| | - Christian Betzel
- Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Building 22a Notkestrasse 85, 22607, Hamburg, Germany.
- The Hamburg Centre for Ultrafast Imaging, University of Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.
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Zhu L, Bu G, Jing L, Shi D, Lee MY, Gonen T, Liu W, Nannenga BL. Structure Determination from Lipidic Cubic Phase Embedded Microcrystals by MicroED. Structure 2020; 28:1149-1159.e4. [PMID: 32735770 PMCID: PMC7544639 DOI: 10.1016/j.str.2020.07.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 06/02/2020] [Accepted: 07/13/2020] [Indexed: 01/22/2023]
Abstract
The lipidic cubic phase (LCP) technique has proved to facilitate the growth of high-quality crystals that are otherwise difficult to grow by other methods. However, the crystal size optimization process could be time and resource consuming, if it ever happens. Therefore, improved techniques for structure determination using these small crystals is an important strategy in diffraction technology development. Microcrystal electron diffraction (MicroED) is a technique that uses a cryo-transmission electron microscopy to collect electron diffraction data and determine high-resolution structures from very thin micro- and nanocrystals. In this work, we have used modified LCP and MicroED protocols to analyze crystals embedded in LCP converted by 2-methyl-2,4-pentanediol or lipase, including Proteinase K crystals grown in solution, cholesterol crystals, and human adenosine A2A receptor crystals grown in LCP. These results set the stage for the use of MicroED to analyze microcrystalline samples grown in LCP, especially for those highly challenging membrane protein targets.
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Affiliation(s)
- Lan Zhu
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA; School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA
| | - Guanhong Bu
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA; School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, USA
| | - Liang Jing
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA; School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA
| | - Dan Shi
- Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Ming-Yue Lee
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA; School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA
| | - Tamir Gonen
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Departments of Biological Chemistry and Physiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Wei Liu
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA; School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA.
| | - Brent L Nannenga
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA; School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, USA.
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Salmaso V, Jacobson KA. In Silico Drug Design for Purinergic GPCRs: Overview on Molecular Dynamics Applied to Adenosine and P2Y Receptors. Biomolecules 2020; 10:E812. [PMID: 32466404 PMCID: PMC7356333 DOI: 10.3390/biom10060812] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/21/2020] [Accepted: 05/22/2020] [Indexed: 12/14/2022] Open
Abstract
Molecular modeling has contributed to drug discovery for purinergic GPCRs, including adenosine receptors (ARs) and P2Y receptors (P2YRs). Experimental structures and homology modeling have proven to be useful in understanding and predicting structure activity relationships (SAR) of agonists and antagonists. This review provides an excursus on molecular dynamics (MD) simulations applied to ARs and P2YRs. The binding modes of newly synthesized A1AR- and A3AR-selective nucleoside derivatives, potentially of use against depression and inflammation, respectively, have been predicted to recapitulate their SAR and the species dependence of A3AR affinity. P2Y12R and P2Y1R crystallographic structures, respectively, have provided a detailed understanding of the recognition of anti-inflammatory P2Y14R antagonists and a large group of allosteric and orthosteric antagonists of P2Y1R, an antithrombotic and neuroprotective target. MD of A2AAR (an anticancer and neuroprotective target), A3AR, and P2Y1R has identified microswitches that are putatively involved in receptor activation. The approach pathways of different ligands toward A2AAR and P2Y1R binding sites have also been explored. A1AR, A2AAR, and A3AR were utilizes to study allosteric phenomena, but locating the binding site of structurally diverse allosteric modulators, such as an A3AR enhancer LUF6000, is challenging. Ligand residence time, a predictor of in vivo efficacy, and the structural role of water were investigated through A2AAR MD simulations. Thus, new MD and other modeling algorithms have contributed to purinergic GPCR drug discovery.
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Affiliation(s)
| | - Kenneth A. Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA;
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Insights into adenosine A2A receptor activation through cooperative modulation of agonist and allosteric lipid interactions. PLoS Comput Biol 2020; 16:e1007818. [PMID: 32298258 PMCID: PMC7188303 DOI: 10.1371/journal.pcbi.1007818] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 04/28/2020] [Accepted: 03/23/2020] [Indexed: 12/18/2022] Open
Abstract
The activation process of G protein-coupled receptors (GPCRs) has been extensively studied, both experimentally and computationally. In particular, Molecular Dynamics (MD) simulations have proven useful in exploring GPCR conformational space. The typical behaviour of class A GPCRs, when subjected to unbiased MD simulations from their crystallized inactive state, is to fluctuate between inactive and intermediate(s) conformations, even with bound agonist. Fully active conformation(s) are rarely stabilized unless a G protein is also bound. Despite several crystal structures of the adenosine A2a receptor (A2aR) having been resolved in complex with co-crystallized agonists and Gs protein, its agonist-mediated activation process is still not completely understood. In order to thoroughly examine the conformational landscape of A2aR activation, we performed unbiased microsecond-length MD simulations in quadruplicate, starting from the inactive conformation either in apo or with bound agonists: endogenous adenosine or synthetic NECA, embedded in two homogeneous phospholipid membranes: 1,2-dioleoyl-sn-glycerol-3-phosphoglycerol (DOPG) or 1,2-dioleoyl-sn-glycerol-3-phosphocholine (DOPC). In DOPC with bound adenosine or NECA, we observe transition to an intermediate receptor conformation consistent with the known adenosine-bound crystal state. In apo state in DOPG, two different intermediate conformations are obtained. One is similar to that observed with bound adenosine in DOPC, while the other is closer to the active state but not yet fully active. Exclusively, in DOPG with bound adenosine or NECA, we reproducibly identify receptor conformations with fully active features, which are able to dock Gs protein. These different receptor conformations can be attributed to the action/absence of agonist and phospholipid-mediated allosteric effects on the intracellular side of the receptor.
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36
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Viscosity-adjustable grease matrices for serial nanocrystallography. Sci Rep 2020; 10:1371. [PMID: 31992735 PMCID: PMC6987181 DOI: 10.1038/s41598-020-57675-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 12/30/2019] [Indexed: 11/26/2022] Open
Abstract
Serial femtosecond crystallography (SFX) has enabled determination of room temperature structures of proteins with minimum radiation damage. A highly viscous grease matrix acting as a crystal carrier for serial sample loading at a low flow rate of ~0.5 μl min−1 was introduced into the beam path of X-ray free-electron laser. This matrix makes it possible to determine the protein structure with a sample consumption of less than 1 mg of the protein. The viscosity of the matrix is an important factor in maintaining a continuous and stable sample column from a nozzle of a high viscosity micro-extrusion injector for serial sample loading. Using conventional commercial grease (an oil-based, viscous agent) with insufficient control of viscosity in a matrix often gives an unexpectedly low viscosity, providing an unstable sample stream, with effects such as curling of the stream. Adjustment of the grease viscosity is extremely difficult since the commercial grease contains unknown compounds, which may act as unexpected inhibitors of proteins. This study introduces two novel grease matrix carriers comprising known compounds with a viscosity higher than that of conventional greases, to determine the proteinase K structure from nano-/microcrystals.
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Role of cholesterol-mediated effects in GPCR heterodimers. Chem Phys Lipids 2019; 227:104852. [PMID: 31866438 DOI: 10.1016/j.chemphyslip.2019.104852] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 12/16/2019] [Accepted: 12/16/2019] [Indexed: 12/19/2022]
Abstract
G protein-coupled receptors (GPCRs) are transmembrane receptors that mediate a large number of cellular responses. The organization of GPCRs into dimers and higher-order oligomers is known to allow a larger repertoire of downstream signaling events. In this context, a crosstalk between the adenosine and dopamine receptors has been reported, indicating the presence of heterodimers that are functionally relevant. In this paper, we explored the effect of membrane cholesterol on the adenosine2A (A2A) and dopamine D3 (D3) receptors using coarse-grain molecular dynamics simulations. We analyzed cholesterol interaction sites on the A2A receptor and were able to reproduce the sites indicated by crystallography and previous atomistic simulations. We predict novel cholesterol interaction sites on the D3 receptor that could be important in the reported cholesterol sensitivity in receptor function. Further, we analyzed the formation of heterodimers between the two receptors. Our results suggest that membrane cholesterol modulates the relative population of several co-existing heterodimer conformations. Both direct receptor-cholesterol interaction and indirect membrane effects contribute toward the modulation of heterodimer conformations. These results constitute one of the first examples of modulation of GPCR hetero-dimerization by membrane cholesterol, and could prove to be useful in designing better therapeutic strategies.
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Ishchenko A, Stauch B, Han GW, Batyuk A, Shiriaeva A, Li C, Zatsepin N, Weierstall U, Liu W, Nango E, Nakane T, Tanaka R, Tono K, Joti Y, Iwata S, Moraes I, Gati C, Cherezov V. Toward G protein-coupled receptor structure-based drug design using X-ray lasers. IUCRJ 2019; 6:1106-1119. [PMID: 31709066 PMCID: PMC6830214 DOI: 10.1107/s2052252519013137] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 09/23/2019] [Indexed: 06/10/2023]
Abstract
Rational structure-based drug design (SBDD) relies on the availability of a large number of co-crystal structures to map the ligand-binding pocket of the target protein and use this information for lead-compound optimization via an iterative process. While SBDD has proven successful for many drug-discovery projects, its application to G protein-coupled receptors (GPCRs) has been limited owing to extreme difficulties with their crystallization. Here, a method is presented for the rapid determination of multiple co-crystal structures for a target GPCR in complex with various ligands, taking advantage of the serial femtosecond crystallography approach, which obviates the need for large crystals and requires only submilligram quantities of purified protein. The method was applied to the human β2-adrenergic receptor, resulting in eight room-temperature co-crystal structures with six different ligands, including previously unreported structures with carvedilol and propranolol. The generality of the proposed method was tested with three other receptors. This approach has the potential to enable SBDD for GPCRs and other difficult-to-crystallize membrane proteins.
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Affiliation(s)
- Andrii Ishchenko
- Bridge Institute, Departments of Chemistry and Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Benjamin Stauch
- Bridge Institute, Departments of Chemistry and Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Gye Won Han
- Bridge Institute, Departments of Chemistry and Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Alexander Batyuk
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Anna Shiriaeva
- Bridge Institute, Departments of Chemistry and Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Chufeng Li
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Nadia Zatsepin
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Uwe Weierstall
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Wei Liu
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Eriko Nango
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Takanori Nakane
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo, Tokyo 113-0032, Japan
| | - Rie Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Yasumasa Joti
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - So Iwata
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Isabel Moraes
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, England
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0FA, England
| | - Cornelius Gati
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
- Biosciences Division, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Vadim Cherezov
- Bridge Institute, Departments of Chemistry and Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
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Zarzycka B, Zaidi SA, Roth BL, Katritch V. Harnessing Ion-Binding Sites for GPCR Pharmacology. Pharmacol Rev 2019; 71:571-595. [PMID: 31551350 PMCID: PMC6782022 DOI: 10.1124/pr.119.017863] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Endogenous ions play important roles in the function and pharmacology of G-protein coupled receptors (GPCRs). Historically the evidence for ionic modulation of GPCR function dates to 1973 with studies of opioid receptors, where it was demonstrated that physiologic concentrations of sodium allosterically attenuated agonist binding. This Na+-selective effect was distinct from effects of other monovalent and divalent cations, with the latter usually counteracting sodium's negative allosteric modulation of binding. Since then, numerous studies documenting the effects of mono- and divalent ions on GPCR function have been published. While ions can act selectively and nonselectively at many sites in different receptors, the discovery of the conserved sodium ion site in class A GPCR structures in 2012 revealed the unique nature of Na+ site, which has emerged as a near-universal site for allosteric modulation of class A GPCR structure and function. In this review, we synthesize and highlight recent advances in the functional, biophysical, and structural characterization of ions bound to GPCRs. Taken together, these findings provide a molecular understanding of the unique roles of Na+ and other ions as GPCR allosteric modulators. We will also discuss how this knowledge can be applied to the redesign of receptors and ligand probes for desired functional and pharmacological profiles. SIGNIFICANCE STATEMENT: The function and pharmacology of GPCRs strongly depend on the presence of mono and divalent ions in experimental assays and in living organisms. Recent insights into the molecular mechanism of this ion-dependent allosterism from structural, biophysical, biochemical, and computational studies provide quantitative understandings of the pharmacological effects of drugs in vitro and in vivo and open new avenues for the rational design of chemical probes and drug candidates with improved properties.
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Affiliation(s)
- Barbara Zarzycka
- Departments of Biological Sciences (B.Z., S.A.Z., V.K.) and Chemistry (V.K.), Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California; and Department of Pharmacology (B.L.R.) and Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy (B.L.R.), University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Saheem A Zaidi
- Departments of Biological Sciences (B.Z., S.A.Z., V.K.) and Chemistry (V.K.), Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California; and Department of Pharmacology (B.L.R.) and Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy (B.L.R.), University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Bryan L Roth
- Departments of Biological Sciences (B.Z., S.A.Z., V.K.) and Chemistry (V.K.), Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California; and Department of Pharmacology (B.L.R.) and Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy (B.L.R.), University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Vsevolod Katritch
- Departments of Biological Sciences (B.Z., S.A.Z., V.K.) and Chemistry (V.K.), Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California; and Department of Pharmacology (B.L.R.) and Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy (B.L.R.), University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
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40
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Standfuss J. Membrane protein dynamics studied by X-ray lasers – or why only time will tell. Curr Opin Struct Biol 2019; 57:63-71. [DOI: 10.1016/j.sbi.2019.02.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 02/04/2019] [Accepted: 02/04/2019] [Indexed: 01/05/2023]
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41
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Zatsepin NA, Li C, Colasurd P, Nannenga BL. The complementarity of serial femtosecond crystallography and MicroED for structure determination from microcrystals. Curr Opin Struct Biol 2019; 58:286-293. [PMID: 31345629 DOI: 10.1016/j.sbi.2019.06.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 06/11/2019] [Accepted: 06/11/2019] [Indexed: 11/19/2022]
Abstract
In recent years, nano and microcrystals have emerged as a valuable source of high-resolution structural information owing to the invention of serial femtosecond crystallography (SFX) with X-ray free electron lasers and microcrystal electron diffraction (MicroED) using electron cryomicroscopes. Once considered useless for structure determination, nano/microcrystals now confer significant advantages for static and time-resolved structure determination from a wide variety of difficult-to-study targets. MicroED has been used to obtain sub-Ångstrom resolution maps in which hydrogen atoms can be clearly resolved from only a few nano/microcrystals, while SFX has been used to probe protein dynamics following reaction initiation on time scales from femtoseconds to minutes. We review these two complementary techniques and their abilities for high-resolution structure determination.
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Affiliation(s)
- Nadia A Zatsepin
- Department of Physics, Arizona State University, P.O. Box 871504, Tempe, AZ 85287, USA
| | - Chufeng Li
- Department of Physics, Arizona State University, P.O. Box 871504, Tempe, AZ 85287, USA
| | - Paige Colasurd
- Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, AZ 85287, USA
| | - Brent L Nannenga
- Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, AZ 85287, USA.
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42
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Hockenberry AJ, Wilke CO. Evolutionary couplings detect side-chain interactions. PeerJ 2019; 7:e7280. [PMID: 31328041 PMCID: PMC6622159 DOI: 10.7717/peerj.7280] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 06/09/2019] [Indexed: 12/19/2022] Open
Abstract
Patterns of amino acid covariation in large protein sequence alignments can inform the prediction of de novo protein structures, binding interfaces, and mutational effects. While algorithms that detect these so-called evolutionary couplings between residues have proven useful for practical applications, less is known about how and why these methods perform so well, and what insights into biological processes can be gained from their application. Evolutionary coupling algorithms are commonly benchmarked by comparison to true structural contacts derived from solved protein structures. However, the methods used to determine true structural contacts are not standardized and different definitions of structural contacts may have important consequences for interpreting the results from evolutionary coupling analyses and understanding their overall utility. Here, we show that evolutionary coupling analyses are significantly more likely to identify structural contacts between side-chain atoms than between backbone atoms. We use both simulations and empirical analyses to highlight that purely backbone-based definitions of true residue–residue contacts (i.e., based on the distance between Cα atoms) may underestimate the accuracy of evolutionary coupling algorithms by as much as 40% and that a commonly used reference point (Cβ atoms) underestimates the accuracy by 10–15%. These findings show that co-evolutionary outcomes differ according to which atoms participate in residue–residue interactions and suggest that accounting for different interaction types may lead to further improvements to contact-prediction methods.
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Affiliation(s)
- Adam J Hockenberry
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Claus O Wilke
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
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43
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Guo G, Zhu P, Fuchs MR, Shi W, Andi B, Gao Y, Hendrickson WA, McSweeney S, Liu Q. Synchrotron microcrystal native-SAD phasing at a low energy. IUCRJ 2019; 6:532-542. [PMID: 31316798 PMCID: PMC6608635 DOI: 10.1107/s2052252519004536] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 04/03/2019] [Indexed: 05/31/2023]
Abstract
De novo structural evaluation of native biomolecules from single-wavelength anomalous diffraction (SAD) is a challenge because of the weakness of the anomalous scattering. The anomalous scattering from relevant native elements - primarily sulfur in proteins and phospho-rus in nucleic acids - increases as the X-ray energy decreases toward their K-edge transitions. Thus, measurements at a lowered X-ray energy are promising for making native SAD routine and robust. For microcrystals with sizes less than 10 µm, native-SAD phasing at synchrotron microdiffraction beamlines is even more challenging because of difficulties in sample manipulation, diffraction data collection and data analysis. Native-SAD analysis from microcrystals by using X-ray free-electron lasers has been demonstrated but has required use of thousands of thousands of microcrystals to achieve the necessary accuracy. Here it is shown that by exploitation of anomalous microdiffraction signals obtained at 5 keV, by the use of polyimide wellmounts, and by an iterative crystal and frame-rejection method, microcrystal native-SAD phasing is possible from as few as about 1 200 crystals. Our results show the utility of low-energy native-SAD phasing with microcrystals at synchrotron microdiffraction beamlines.
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Affiliation(s)
- Gongrui Guo
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
- Photon Science, NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Ping Zhu
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Martin R. Fuchs
- Photon Science, NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Wuxian Shi
- Photon Science, NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Babak Andi
- Photon Science, NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Yuan Gao
- Photon Science, NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Wayne A. Hendrickson
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| | - Sean McSweeney
- Photon Science, NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Qun Liu
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
- Photon Science, NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
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44
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Agrawal N, Chandrasekaran B, Al-Aboudi A. Recent Advances in the In-silico Structure-based and Ligand-based Approaches for the Design and Discovery of Agonists and Antagonists of A2A Adenosine Receptor. Curr Pharm Des 2019; 25:774-782. [DOI: 10.2174/1381612825666190306162006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 02/26/2019] [Indexed: 01/20/2023]
Abstract
A2A receptor belongs to the family of GPCRs, which are the most abundant membrane protein family.
Studies in the last few decades have shown the therapeutic applications of A2A receptor in various diseases. In the
present mini-review, we have discussed the recent progress in the in-silico studies of the A2A receptor. Herein, we
described the different structures of A2A receptor, the discovery of new agonists and antagonists using virtualscreening/
docking, pharmacophore modeling, and QSAR based pharmacophore modeling. We have also discussed
various molecular dynamics (MD) simulations studies of A2A receptor in complex with ligands.
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Affiliation(s)
- Nikhil Agrawal
- College of Health Sciences, University of KwaZulu-Natal, P. O. Box: 4000, Westville, Durban, South Africa
| | - Balakumar Chandrasekaran
- College of Health Sciences, University of KwaZulu-Natal, P. O. Box: 4000, Westville, Durban, South Africa
| | - Amal Al-Aboudi
- Faculty of Science, The University of Jordan, Amman, 11942, Jordan
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45
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Mishin A, Gusach A, Luginina A, Marin E, Borshchevskiy V, Cherezov V. An outlook on using serial femtosecond crystallography in drug discovery. Expert Opin Drug Discov 2019; 14:933-945. [PMID: 31184514 DOI: 10.1080/17460441.2019.1626822] [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] [Indexed: 12/20/2022]
Abstract
Introduction: X-ray crystallography has made important contributions to modern drug development but its application to many important drug targets has been extremely challenging. The recent emergence of X-ray free electron lasers (XFELs) and advancements in serial femtosecond crystallography (SFX) have offered new opportunities to overcome limitations of traditional crystallography to accelerate the structure-based drug discovery (SBDD) process. Areas covered: In this review, the authors describe the general principles of X-ray generation and the main properties of XFEL beams, outline details of SFX data collection and processing, and summarize the progress in the development of associated instrumentation for sample delivery and X-ray detection. An overview of the SFX applications to various important drug targets such as membrane proteins is also provided. Expert opinion: While SFX has already made clear advancements toward the understanding of the structure and dynamics of several major drug targets, its robust application in SBDD still needs further developments of new high-throughput techniques for sample production, automation of crystal delivery and data collection, as well as for processing and storage of large amounts of data. The expansion of the available XFEL beamtime is a key to the success of SFX in SBDD.
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Affiliation(s)
- Alexey Mishin
- a Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology , Dolgoprudny , Russia
| | - Anastasiia Gusach
- a Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology , Dolgoprudny , Russia
| | - Aleksandra Luginina
- a Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology , Dolgoprudny , Russia
| | - Egor Marin
- a Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology , Dolgoprudny , Russia
| | - Valentin Borshchevskiy
- a Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology , Dolgoprudny , Russia
| | - Vadim Cherezov
- a Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology , Dolgoprudny , Russia.,b Bridge Institute, Departments of Chemistry and Biological Sciences, University of Southern California , Los Angeles , CA , USA
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46
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Wink LH, Baker DL, Cole JA, Parrill AL. A benchmark study of loop modeling methods applied to G protein-coupled receptors. J Comput Aided Mol Des 2019; 33:573-595. [PMID: 31123958 DOI: 10.1007/s10822-019-00196-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 03/12/2019] [Indexed: 11/25/2022]
Abstract
G protein-coupled receptors (GPCR) are important drug discovery targets. Despite progress, many GPCR structures have not yet been solved. For these targets, comparative modeling is used in virtual ligand screening to prioritize experimental efforts. However, the structure of extracellular loop 2 (ECL2) is often poorly predicted. This is significant due to involvement of ECL2 in ligand binding for many Class A GPCR. Here we examine the performance of loop modeling protocols available in the Rosetta (cyclic coordinate descent [CCD], KIC with fragments [KICF] and next generation KIC [NGK]) and Molecular Operating Environment (MOE) software suites (de novo search). ECL2 from GPCR crystal structures served as the structure prediction targets and were divided into four sets depending on loop length. Results suggest that KICF and NGK sampled and scored more loop models with sub-angstrom and near-atomic accuracy than CCD or de novo search for loops of 24 or fewer residues. None of the methods were able to sample loop conformations with near-atomic accuracy for the longest targets ranging from 25 to 32 residues based on 1000 models generated. For these long loop targets, increased conformational sampling is necessary. The strongly conserved disulfide bond between Cys3.25 and Cys45.50 in ECL2 proved an effective filter. Setting an upper limit of 5.1 Å on the S-S distance improved the lowest RMSD model included in the top 10 scored structures in Groups 1-4 on average between 0.33 and 1.27 Å. Disulfide bond formation and geometry optimization of ECL2 provided an additional incremental benefit in structure quality.
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Affiliation(s)
- Lee H Wink
- Department of Chemistry, The University of Memphis, Memphis, TN, 38152, USA
| | - Daniel L Baker
- Department of Chemistry, The University of Memphis, Memphis, TN, 38152, USA
| | - Judith A Cole
- Department of Biological Sciences, The University of Memphis, Memphis, TN, 38152, USA
| | - Abby L Parrill
- Department of Chemistry, The University of Memphis, Memphis, TN, 38152, USA.
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Martin-Garcia JM, Zhu L, Mendez D, Lee MY, Chun E, Li C, Hu H, Subramanian G, Kissick D, Ogata C, Henning R, Ishchenko A, Dobson Z, Zhang S, Weierstall U, Spence JCH, Fromme P, Zatsepin NA, Fischetti RF, Cherezov V, Liu W. High-viscosity injector-based pink-beam serial crystallography of microcrystals at a synchrotron radiation source. IUCRJ 2019; 6:412-425. [PMID: 31098022 PMCID: PMC6503920 DOI: 10.1107/s205225251900263x] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 02/20/2019] [Indexed: 05/29/2023]
Abstract
Since the first successful serial crystallography (SX) experiment at a synchrotron radiation source, the popularity of this approach has continued to grow showing that third-generation synchrotrons can be viable alternatives to scarce X-ray free-electron laser sources. Synchrotron radiation flux may be increased ∼100 times by a moderate increase in the bandwidth ('pink beam' conditions) at some cost to data analysis complexity. Here, we report the first high-viscosity injector-based pink-beam SX experiments. The structures of proteinase K (PK) and A2A adenosine receptor (A2AAR) were determined to resolutions of 1.8 and 4.2 Å using 4 and 24 consecutive 100 ps X-ray pulse exposures, respectively. Strong PK data were processed using existing Laue approaches, while weaker A2AAR data required an alternative data-processing strategy. This demonstration of the feasibility presents new opportunities for time-resolved experiments with microcrystals to study structural changes in real time at pink-beam synchrotron beamlines worldwide.
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Affiliation(s)
- Jose M. Martin-Garcia
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA
| | - Lan Zhu
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA
| | - Derek Mendez
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, 550 East Tyler Drive, Tempe, AZ 85287, USA
| | - Ming-Yue Lee
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA
| | - Eugene Chun
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA
| | - Chufeng Li
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, 550 East Tyler Drive, Tempe, AZ 85287, USA
| | - Hao Hu
- Department of Physics, Arizona State University, 550 East Tyler Drive, Tempe, AZ 85287, USA
| | - Ganesh Subramanian
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, 550 East Tyler Drive, Tempe, AZ 85287, USA
| | - David Kissick
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Ave, Lemont, IL 90439, USA
| | - Craig Ogata
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Ave, Lemont, IL 90439, USA
| | - Robert Henning
- Center for Advanced Radiation Sources, The University of Chicago, Argonne National Laboratory, 9700 South Cass Ave, Lemont, IL 90439, USA
| | - Andrii Ishchenko
- Department of Chemistry, Bridge Institute, University of Southern California, 1002 Childs Way, Los Angeles, CA 90089, USA
| | - Zachary Dobson
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA
| | - Shangji Zhang
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA
| | - Uwe Weierstall
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, 550 East Tyler Drive, Tempe, AZ 85287, USA
| | - John C. H. Spence
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, 550 East Tyler Drive, Tempe, AZ 85287, USA
| | - Petra Fromme
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA
| | - Nadia A. Zatsepin
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, 550 East Tyler Drive, Tempe, AZ 85287, USA
| | - Robert F. Fischetti
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Ave, Lemont, IL 90439, USA
| | - Vadim Cherezov
- Department of Chemistry, Bridge Institute, University of Southern California, 1002 Childs Way, Los Angeles, CA 90089, USA
| | - Wei Liu
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA
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McGraw C, Yang L, Levental I, Lyman E, Robinson AS. Membrane cholesterol depletion reduces downstream signaling activity of the adenosine A 2A receptor. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:760-767. [PMID: 30629951 DOI: 10.1016/j.bbamem.2019.01.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 12/14/2018] [Accepted: 01/02/2019] [Indexed: 12/11/2022]
Abstract
Cholesterol has been shown to modulate the activity of multiple G Protein-coupled receptors (GPCRs), yet whether cholesterol acts through specific interactions, indirectly via modifications to the membrane, or via both mechanisms is not well understood. High-resolution crystal structures of GPCRs have identified bound cholesterols; based on a β2-adrenergic receptor (β2AR) structure bound to cholesterol and the presence of conserved amino acids in class A receptors, the cholesterol consensus motif (CCM) was identified. Here in mammalian cells expressing the adenosine A2A receptor (A2AR), ligand dependent production of cAMP is reduced following membrane cholesterol depletion with methyl-beta-cyclodextrin (MβCD), indicating that A2AR signaling is dependent on cholesterol. In contrast, ligand binding is not dependent on cholesterol depletion. All-atom molecular simulations suggest that cholesterol interacts specifically with the CCM when the receptor is in an active state, but not when in an inactive state. Taken together, the data support a model of receptor state-dependent binding between cholesterol and the CCM, which could facilitate both G-protein coupling and downstream signaling of A2AR.
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Affiliation(s)
- Claire McGraw
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, LA, United States
| | - Lewen Yang
- Department of Physics and Astronomy, University of Delaware, Newark, DE, United States
| | - Ilya Levental
- Department of Integrative Biology and Pharmacology, University of Texas- Houston, Houston, TX, United States
| | - Edward Lyman
- Department of Physics and Astronomy, University of Delaware, Newark, DE, United States
| | - Anne Skaja Robinson
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, LA, United States.
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Johnson JM, Hays FA. High-Throughput Protein Production of Membrane Proteins in Saccharomyces cerevisiae. Methods Mol Biol 2019; 2025:227-259. [PMID: 31267456 DOI: 10.1007/978-1-4939-9624-7_11] [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] [Indexed: 06/09/2023]
Abstract
This chapter outlines a protocol to assess viability for large-scale protein production and purification for selected targets from an initial medium-throughput cloning strategy. Thus, one can assess a broad number of potential candidate proteins, mutants, or expression variants using an empirically minimalistic approach. In addition, a key output from this protocol is utilization of Saccharomyces cerevisiae as a means for the efficient screening and production of purified proteins. The primary focus in this protocol is overexpression of polytopic integral membrane proteins though methods can be equally applied to soluble proteins. The protocol starts with outlining high-throughput (sans robotics) cloning of expression proteins into a dual-tag yeast expression plasmid. These membrane proteins are then screened for expression level, detergent solubilization, initial purity, and chromatography characteristics. Both small- and large-scale expression methods are discussed along with fermentation.
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Affiliation(s)
- Jennifer M Johnson
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Franklin A Hays
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- Harold Hamm Diabetes Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
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50
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Kiriakidi S, Kolocouris A, Liapakis G, Ikram S, Durdagi S, Mavromoustakos T. Effects of Cholesterol on GPCR Function: Insights from Computational and Experimental Studies. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1135:89-103. [DOI: 10.1007/978-3-030-14265-0_5] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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