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Huang CY, Aumonier S, Olieric V, Wang M. Cryo2RT: a high-throughput method for room-temperature macromolecular crystallography from cryo-cooled crystals. Acta Crystallogr D Struct Biol 2024; 80:620-628. [PMID: 39052318 DOI: 10.1107/s2059798324006697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 07/08/2024] [Indexed: 07/27/2024] Open
Abstract
Advances in structural biology have relied heavily on synchrotron cryo-crystallography and cryogenic electron microscopy to elucidate biological processes and for drug discovery. However, disparities between cryogenic and room-temperature (RT) crystal structures pose challenges. Here, Cryo2RT, a high-throughput RT data-collection method from cryo-cooled crystals that leverages the cryo-crystallography workflow, is introduced. Tested on endothiapepsin crystals with four soaked fragments, thaumatin and SARS-CoV-2 3CLpro, Cryo2RT reveals unique ligand-binding poses, offers a comparable throughput to cryo-crystallography and eases the exploration of structural dynamics at various temperatures.
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Affiliation(s)
- Chia Ying Huang
- Swiss Light Source, Center for Photon Science, Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | - Sylvain Aumonier
- Swiss Light Source, Center for Photon Science, Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | - Vincent Olieric
- Swiss Light Source, Center for Photon Science, Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | - Meitian Wang
- Swiss Light Source, Center for Photon Science, Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
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2
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Szwabowski GL, Griffing M, Mugabe EJ, O’Malley D, Baker LN, Baker DL, Parrill AL. G Protein-Coupled Receptor-Ligand Pose and Functional Class Prediction. Int J Mol Sci 2024; 25:6876. [PMID: 38999982 PMCID: PMC11241240 DOI: 10.3390/ijms25136876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 06/13/2024] [Accepted: 06/19/2024] [Indexed: 07/14/2024] Open
Abstract
G protein-coupled receptor (GPCR) transmembrane protein family members play essential roles in physiology. Numerous pharmaceuticals target GPCRs, and many drug discovery programs utilize virtual screening (VS) against GPCR targets. Improvements in the accuracy of predicting new molecules that bind to and either activate or inhibit GPCR function would accelerate such drug discovery programs. This work addresses two significant research questions. First, do ligand interaction fingerprints provide a substantial advantage over automated methods of binding site selection for classical docking? Second, can the functional status of prospective screening candidates be predicted from ligand interaction fingerprints using a random forest classifier? Ligand interaction fingerprints were found to offer modest advantages in sampling accurate poses, but no substantial advantage in the final set of top-ranked poses after scoring, and, thus, were not used in the generation of the ligand-receptor complexes used to train and test the random forest classifier. A binary classifier which treated agonists, antagonists, and inverse agonists as active and all other ligands as inactive proved highly effective in ligand function prediction in an external test set of GPR31 and TAAR2 candidate ligands with a hit rate of 82.6% actual actives within the set of predicted actives.
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Affiliation(s)
| | | | | | | | | | - Daniel L. Baker
- Department of Chemistry, University of Memphis, Memphis, TN 38152, USA; (G.L.S.); (M.G.); (E.J.M.); (D.O.); (L.N.B.)
| | - Abby L. Parrill
- Department of Chemistry, University of Memphis, Memphis, TN 38152, USA; (G.L.S.); (M.G.); (E.J.M.); (D.O.); (L.N.B.)
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3
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Do HN, Wang J, Miao Y. Deep Learning Dynamic Allostery of G-Protein-Coupled Receptors. JACS AU 2023; 3:3165-3180. [PMID: 38034960 PMCID: PMC10685416 DOI: 10.1021/jacsau.3c00503] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 10/10/2023] [Accepted: 10/18/2023] [Indexed: 12/02/2023]
Abstract
G-protein-coupled receptors (GPCRs) make up the largest superfamily of human membrane proteins and represent primary targets of ∼1/3 of currently marketed drugs. Allosteric modulators have emerged as more selective drug candidates compared with orthosteric agonists and antagonists. However, many X-ray and cryo-EM structures of GPCRs resolved so far exhibit negligible differences upon the binding of positive and negative allosteric modulators (PAMs and NAMs). The mechanism of dynamic allosteric modulation in GPCRs remains unclear. In this work, we have systematically mapped dynamic changes in free energy landscapes of GPCRs upon binding of allosteric modulators using the Gaussian accelerated molecular dynamics (GaMD), deep learning (DL), and free energy prOfiling Workflow (GLOW). GaMD simulations were performed for a total of 66 μs on 44 GPCR systems in the presence and absence of the modulator. DL and free energy calculations revealed significantly reduced dynamic fluctuations and conformational space of GPCRs upon modulator binding. While the modulator-free GPCRs often sampled multiple low-energy conformational states, the NAMs and PAMs confined the inactive and active agonist-G-protein-bound GPCRs, respectively, to mostly only one specific conformation for signaling. Such cooperative effects were significantly reduced for binding of the selective modulators to "non-cognate" receptor subtypes. Therefore, GPCR allostery exhibits a dynamic "conformational selection" mechanism. In the absence of available modulator-bound structures as for most current GPCRs, it is critical to use a structural ensemble of representative GPCR conformations rather than a single structure for compound docking ("ensemble docking"), which will potentially improve structure-based design of novel allosteric drugs of GPCRs.
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Affiliation(s)
| | - Jinan Wang
- Computational Biology Program
and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047, United States
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4
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Smithers L, Degtjarik O, Weichert D, Huang CY, Boland C, Bowen K, Oluwole A, Lutomski C, Robinson CV, Scanlan EM, Wang M, Olieric V, Shalev-Benami M, Caffrey M. Structure snapshots reveal the mechanism of a bacterial membrane lipoprotein N-acyltransferase. SCIENCE ADVANCES 2023; 9:eadf5799. [PMID: 37390210 PMCID: PMC10313180 DOI: 10.1126/sciadv.adf5799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 05/26/2023] [Indexed: 07/02/2023]
Abstract
Bacterial lipoproteins (BLPs) decorate the surface of membranes in the cell envelope. They function in membrane assembly and stability, as enzymes, and in transport. The final enzyme in the BLP synthesis pathway is the apolipoprotein N-acyltransferase, Lnt, which is proposed to act by a ping-pong mechanism. Here, we use x-ray crystallography and cryo-electron microscopy to chart the structural changes undergone during the progress of the enzyme through the reaction. We identify a single active site that has evolved to bind, individually and sequentially, substrates that satisfy structural and chemical criteria to position reactive parts next to the catalytic triad for reaction. This study validates the ping-pong mechanism, explains the molecular bases for Lnt's substrate promiscuity, and should facilitate the design of antibiotics with minimal off-target effects.
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Affiliation(s)
- Luke Smithers
- School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin D02 R590, Ireland
| | - Oksana Degtjarik
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Dietmar Weichert
- School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin D02 R590, Ireland
| | - Chia-Ying Huang
- Swiss Light Source, Paul Scherrer Institute, CH-5232 Villigen, Switzerland
| | - Coilín Boland
- School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin D02 R590, Ireland
| | - Katherine Bowen
- School of Chemistry, Trinity College Dublin, Dublin D02 R590, Ireland
| | - Abraham Oluwole
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Corinne Lutomski
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Carol V. Robinson
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Eoin M. Scanlan
- School of Chemistry, Trinity College Dublin, Dublin D02 R590, Ireland
| | - Meitian Wang
- Swiss Light Source, Paul Scherrer Institute, CH-5232 Villigen, Switzerland
| | - Vincent Olieric
- Swiss Light Source, Paul Scherrer Institute, CH-5232 Villigen, Switzerland
| | - Moran Shalev-Benami
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Martin Caffrey
- School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin D02 R590, Ireland
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5
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Wang H, Mörman C, Sternke-Hoffmann R, Huang CY, Prota A, Ma P, Luo J. Cu 2+ ions modulate the interaction between α-synuclein and lipid membranes. J Inorg Biochem 2022; 236:111945. [PMID: 35952593 DOI: 10.1016/j.jinorgbio.2022.111945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 07/20/2022] [Accepted: 07/22/2022] [Indexed: 12/15/2022]
Abstract
α-synuclein protein aggregates are the major constituent of Lewy bodies, which is a main pathogenic hallmark of Parkinson's disease. Both lipid membranes and Cu2+ ions can bind to α-synuclein and modulate its aggregation propensity and toxicity. However, the synergistic effect of copper ions and lipid membranes on α-synuclein remains to be explored. Here, we investigate how Cu2+ and α-synuclein simultaneously influence the lipidic structure of lipidic cubic phase(LCP) matrix by using small-angle X-ray scattering. α-Syn proteins destabilize the cubic-Pn3m phase of LCP that can be further recovered after the addition of Cu2 ions even at a low stoichiometric ratio. By using circular dichroism and nuclear magnetic resonance, we also study how lipid membranes and Cu2+ ions impact the secondary structures of α-synuclein at an atomic level. Although the secondary structure of α-synuclein with lipid membranes is not significantly changed to a large extent in the presence of Cu2+ ions, lipid membranes promote the interaction between α-synuclein C-terminus and Cu2+ ions. The modulation of Cu2+ ions and lipid membranes on α-synuclein dynamics and structure may play an important role in the molecular pathogenesis of Parkinson's disease.
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Affiliation(s)
- Hongzhi Wang
- Department of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Cecilia Mörman
- Department of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen, Switzerland; Department of Biosciences and Nutrition, Karolinska Institutet, 141 52 Huddinge, Sweden
| | | | - Chia-Ying Huang
- Swiss Light Source at Paul Scherrer Institut, Forschungstrasse 111, Villigen-PSI, Villigen 5232, Switzerland
| | - Andrea Prota
- Department of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Pikyee Ma
- Department of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Jinghui Luo
- Department of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen, Switzerland.
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6
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Selçuk B, Erol I, Durdağı S, Adebali O. Evolutionary association of receptor-wide amino acids with G protein-coupling selectivity in aminergic GPCRs. Life Sci Alliance 2022; 5:e202201439. [PMID: 35613896 PMCID: PMC9133432 DOI: 10.26508/lsa.202201439] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 11/24/2022] Open
Abstract
G protein-coupled receptors (GPCRs) induce signal transduction pathways through coupling to four main subtypes of G proteins (Gs, Gi, Gq, and G12/13), selectively. However, G protein selective activation mechanisms and residual determinants in GPCRs have remained obscure. Herein, we performed extensive phylogenetic analysis and identified specifically conserved residues for the aminergic receptors having similar coupling profiles. By integrating our methodology of differential evolutionary conservation of G protein-specific amino acids with structural analyses, we identified specific activation networks for Gs, Gi1, Go, and Gq To validate that these networks could determine coupling selectivity we further analyzed Gs-specific activation network and its association with Gs selectivity. Through molecular dynamics simulations, we showed that previously uncharacterized Glycine at position 7x41 plays an important role in receptor activation and it may determine Gs coupling selectivity by facilitating a larger TM6 movement. Finally, we gathered our results into a comprehensive model of G protein selectivity called "sequential switches of activation" describing three main molecular switches controlling GPCR activation: ligand binding, G protein selective activation mechanisms, and G protein contact.
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Affiliation(s)
- Berkay Selçuk
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Ismail Erol
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
- Department of Chemistry, Gebze Technical University, Gebze, Turkey
| | - Serdar Durdağı
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
| | - Ogün Adebali
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
- TÜBiTAK Research Institute for Fundamental Sciences, Gebze, Turkey
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7
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Efimov AV, Meshcheryakova OV, Ryazanov AG. Agonists in the Extended Conformation Stabilize the Active State of β-Adrenoceptors. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:628-639. [PMID: 36154885 DOI: 10.1134/s0006297922070057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 06/21/2022] [Accepted: 06/21/2022] [Indexed: 06/16/2023]
Abstract
In this study, we conducted a comparative analysis of the structure of agonists and antagonists of transmembrane (TM) β-adrenoceptors (β-ARs) and their interactions with the β-ARs and proposed the mechanism of receptor activation. A characteristic feature of agonist and antagonist molecules is the presence of a hydrophobic head (most often, one or two aromatic rings) and a tail with a positively charged amino group. All β-adrenergic agonists have two carbon atoms between the aromatic ring of the head and the nitrogen atom of the amino group. In antagonist molecules, this fragment can be either reduced or increased to four atoms due to the additional carbon and oxygen atoms. The agonist head, as a rule, has two H-bond donors or acceptors in the para- and meta-positions of the aromatic rings, while in the antagonist heads, these donors/acceptors are absent or located in other positions. Analysis of known three-dimensional structures of β-AR complexes with agonists showed that the agonist head forms two H-bonds with the TM5 helix, and the tail forms an ionic bond with the D3.32 residue of the TM3 helix and one or two H-bonds with the TM7 helix. The tail of the antagonist can form similar bonds, but the interaction between the head and the TM5 helix is much weaker. As a result of these interactions, the agonist molecule acquires an extended "strained string" conformation, in contrast to the antagonist molecule, which has a longer, bended, and flexible tail. The "strained string" of the agonist interacts with the TM6 helix (primarily with the W6.48 residue) and turns it, which leads to the opening of the G protein-binding site on the intracellular side of the receptor, while flexible and larger antagonist molecules do not have the same effect on the receptor.
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Affiliation(s)
- Alexander V Efimov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
| | - Olga V Meshcheryakova
- Institute of Biology of the Karelian Research Centre of the Russian Academy of Sciences, 185910 Petrozavodsk, Russia.
| | - Alexey G Ryazanov
- Department of Pharmacology, Rutgers Robert Wood Johnson Medical School, Piscataway, New Jersey, 08854, USA.
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8
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Gildea RJ, Beilsten-Edmands J, Axford D, Horrell S, Aller P, Sandy J, Sanchez-Weatherby J, Owen CD, Lukacik P, Strain-Damerell C, Owen RL, Walsh MA, Winter G. xia2.multiplex: a multi-crystal data-analysis pipeline. Acta Crystallogr D Struct Biol 2022; 78:752-769. [PMID: 35647922 PMCID: PMC9159281 DOI: 10.1107/s2059798322004399] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 04/25/2022] [Indexed: 11/11/2022] Open
Abstract
In macromolecular crystallography, radiation damage limits the amount of data that can be collected from a single crystal. It is often necessary to merge data sets from multiple crystals; for example, small-wedge data collections from micro-crystals, in situ room-temperature data collections and data collection from membrane proteins in lipidic mesophases. Whilst the indexing and integration of individual data sets may be relatively straightforward with existing software, merging multiple data sets from small wedges presents new challenges. The identification of a consensus symmetry can be problematic, particularly in the presence of a potential indexing ambiguity. Furthermore, the presence of non-isomorphous or poor-quality data sets may reduce the overall quality of the final merged data set. To facilitate and help to optimize the scaling and merging of multiple data sets, a new program, xia2.multiplex, has been developed which takes data sets individually integrated with DIALS and performs symmetry analysis, scaling and merging of multi-crystal data sets. xia2.multiplex also performs analysis of various pathologies that typically affect multi-crystal data sets, including non-isomorphism, radiation damage and preferential orientation. After the description of a number of use cases, the benefit of xia2.multiplex is demonstrated within a wider autoprocessing framework in facilitating a multi-crystal experiment collected as part of in situ room-temperature fragment-screening experiments on the SARS-CoV-2 main protease.
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Affiliation(s)
- Richard J. Gildea
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - James Beilsten-Edmands
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Danny Axford
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Sam Horrell
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, United Kingdom
| | - Pierre Aller
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - James Sandy
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Juan Sanchez-Weatherby
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - C. David Owen
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, United Kingdom
| | - Petra Lukacik
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, United Kingdom
| | - Claire Strain-Damerell
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, United Kingdom
| | - Robin L. Owen
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Martin A. Walsh
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, United Kingdom
| | - Graeme Winter
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
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Killer M, Wald J, Pieprzyk J, Marlovits TC, Löw C. Structural snapshots of human PepT1 and PepT2 reveal mechanistic insights into substrate and drug transport across epithelial membranes. SCIENCE ADVANCES 2021; 7:eabk3259. [PMID: 34730990 PMCID: PMC8565842 DOI: 10.1126/sciadv.abk3259] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The uptake of peptides in mammals plays a crucial role in nutrition and inflammatory diseases. This process is mediated by promiscuous transporters of the solute carrier family 15, which form part of the major facilitator superfamily. Besides the uptake of short peptides, peptide transporter 1 (PepT1) is a highly abundant drug transporter in the intestine and represents a major route for oral drug delivery. PepT2 also allows renal drug reabsorption from ultrafiltration and brain-to-blood efflux of neurotoxic compounds. Here, we present cryogenic electron microscopy (cryo-EM) structures of human PepT1 and PepT2 captured in four different states throughout the transport cycle. The structures reveal the architecture of human peptide transporters and provide mechanistic insights into substrate recognition and conformational transitions during transport. This may support future drug design efforts to increase the bioavailability of different drugs in the human body.
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Affiliation(s)
- Maxime Killer
- Centre for Structural Systems Biology (CSSB), Notkestrasse 85, D-22607 Hamburg, Germany
- European Molecular Biology Laboratory (EMBL), Hamburg Unit c/o Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, D-22607 Hamburg, Germany
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Faculty of Biosciences, Im Neuenheimer Feld 234, D-69120 Heidelberg, Germany
| | - Jiri Wald
- Centre for Structural Systems Biology (CSSB), Notkestrasse 85, D-22607 Hamburg, Germany
- Institute of Structural and Systems Biology, University Medical Center Hamburg-Eppendorf, Notkestrasse 85, D-22607 Hamburg, Germany
- Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, D-22607 Hamburg, Germany
| | - Joanna Pieprzyk
- Centre for Structural Systems Biology (CSSB), Notkestrasse 85, D-22607 Hamburg, Germany
- European Molecular Biology Laboratory (EMBL), Hamburg Unit c/o Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, D-22607 Hamburg, Germany
| | - Thomas C. Marlovits
- Centre for Structural Systems Biology (CSSB), Notkestrasse 85, D-22607 Hamburg, Germany
- Institute of Structural and Systems Biology, University Medical Center Hamburg-Eppendorf, Notkestrasse 85, D-22607 Hamburg, Germany
- Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, D-22607 Hamburg, Germany
| | - Christian Löw
- Centre for Structural Systems Biology (CSSB), Notkestrasse 85, D-22607 Hamburg, Germany
- European Molecular Biology Laboratory (EMBL), Hamburg Unit c/o Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, D-22607 Hamburg, Germany
- Corresponding author.
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10
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Healey RD, Basu S, Humm AS, Leyrat C, Cong X, Golebiowski J, Dupeux F, Pica A, Granier S, Márquez JA. An automated platform for structural analysis of membrane proteins through serial crystallography. CELL REPORTS METHODS 2021; 1:None. [PMID: 34723237 PMCID: PMC8545655 DOI: 10.1016/j.crmeth.2021.100102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/07/2021] [Accepted: 09/22/2021] [Indexed: 11/01/2022]
Abstract
Membrane proteins are central to many pathophysiological processes, yet remain very difficult to analyze structurally. Moreover, high-throughput structure-based drug discovery has not yet been exploited for membrane proteins because of lack of automation. Here, we present a facile and versatile platform for in meso membrane protein crystallization, enabling rapid atomic structure determination at both cryogenic and room temperatures. We apply this approach to human integral membrane proteins, which allowed us to identify different conformational states of intramembrane enzyme-product complexes and analyze by molecular dynamics simulations the structural dynamics of the ADIPOR2 integral membrane protein. Finally, we demonstrate an automated pipeline combining high-throughput microcrystal soaking, automated laser-based harvesting, and serial crystallography, enabling screening of small-molecule libraries with membrane protein crystals grown in meso. This approach brings needed automation to this important class of drug targets and enables high-throughput structure-based ligand discovery with membrane proteins.
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Affiliation(s)
- Robert D. Healey
- IGF, University of Montpellier, CNRS, INSERM, 34094 Montpellier, France
| | - Shibom Basu
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Anne-Sophie Humm
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Cedric Leyrat
- IGF, University of Montpellier, CNRS, INSERM, 34094 Montpellier, France
| | - Xiaojing Cong
- IGF, University of Montpellier, CNRS, INSERM, 34094 Montpellier, France
| | - Jérôme Golebiowski
- Institute of Chemistry of Nice UMR7272, Université Côte d’Azur, CNRS, 28 Avenue Valrose, 06108 Nice, France
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Technology, 711-873 Daegu, South Korea
| | - Florine Dupeux
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38000 Grenoble, France
- Institut de Biologie Structurale, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Andrea Pica
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38000 Grenoble, France
- ALPX S.A.S. 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Sébastien Granier
- IGF, University of Montpellier, CNRS, INSERM, 34094 Montpellier, France
| | - José Antonio Márquez
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38000 Grenoble, France
- ALPX S.A.S. 71 Avenue des Martyrs, 38000 Grenoble, France
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11
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Martiel I, Beale JH, Karpik A, Huang CY, Vera L, Olieric N, Wranik M, Tsai CJ, Mühle J, Aurelius O, John J, Högbom M, Wang M, Marsh M, Padeste C. Versatile microporous polymer-based supports for serial macromolecular crystallography. Acta Crystallogr D Struct Biol 2021; 77:1153-1167. [PMID: 34473086 PMCID: PMC8411977 DOI: 10.1107/s2059798321007324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 07/15/2021] [Indexed: 11/10/2022] Open
Abstract
Serial data collection has emerged as a major tool for data collection at state-of-the-art light sources, such as microfocus beamlines at synchrotrons and X-ray free-electron lasers. Challenging targets, characterized by small crystal sizes, weak diffraction and stringent dose limits, benefit most from these methods. Here, the use of a thin support made of a polymer-based membrane for performing serial data collection or screening experiments is demonstrated. It is shown that these supports are suitable for a wide range of protein crystals suspended in liquids. The supports have also proved to be applicable to challenging cases such as membrane proteins growing in the sponge phase. The sample-deposition method is simple and robust, as well as flexible and adaptable to a variety of cases. It results in an optimally thin specimen providing low background while maintaining minute amounts of mother liquor around the crystals. The 2 × 2 mm area enables the deposition of up to several microlitres of liquid. Imaging and visualization of the crystals are straightforward on the highly transparent membrane. Thanks to their affordable fabrication, these supports have the potential to become an attractive option for serial experiments at synchrotrons and free-electron lasers.
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Affiliation(s)
- Isabelle Martiel
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - John H. Beale
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Agnieszka Karpik
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
- Institute of Polymer Nanotechnology (INKA), FHNW University of Applied Sciences and Arts Northwestern Switzerland, 5210 Windisch, Switzerland
| | - Chia-Ying Huang
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Laura Vera
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Natacha Olieric
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Maximilian Wranik
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Ching-Ju Tsai
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Jonas Mühle
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Oskar Aurelius
- Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden
- MAX IV Laboratory, Lund University, Fotongatan 2, 224 84 Lund, Sweden
| | - Juliane John
- Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden
| | - Meitian Wang
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - May Marsh
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Celestino Padeste
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
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12
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Guo L, Fan XY, Qiao X, Montell C, Huang J. An octopamine receptor confers selective toxicity of amitraz on honeybees and Varroa mites. eLife 2021; 10:68268. [PMID: 34263722 PMCID: PMC8313232 DOI: 10.7554/elife.68268] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 07/11/2021] [Indexed: 12/30/2022] Open
Abstract
The Varroa destructor mite is a devastating parasite of Apis mellifera honeybees. They can cause colonies to collapse by spreading viruses and feeding on the fat reserves of adults and larvae. Amitraz is used to control mites due to its low toxicity to bees; however, the mechanism of bee resistance to amitraz remains unknown. In this study, we found that amitraz and its major metabolite potently activated all four mite octopamine receptors. Behavioral assays using Drosophila null mutants of octopamine receptors identified one receptor subtype Octβ2R as the sole target of amitraz in vivo. We found that thermogenetic activation of octβ2R-expressing neurons mimics amitraz poisoning symptoms in target pests. We next confirmed that the mite Octβ2R was more sensitive to amitraz and its metabolite than the bee Octβ2R in pharmacological assays and transgenic flies. Furthermore, replacement of three bee-specific residues with the counterparts in the mite receptor increased amitraz sensitivity of the bee Octβ2R, indicating that the relative insensitivity of their receptor is the major mechanism for honeybees to resist amitraz. The present findings have important implications for resistance management and the design of safer insecticides that selectively target pests while maintaining low toxicity to non-target pollinators.
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Affiliation(s)
- Lei Guo
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Xin-Yu Fan
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Xiaomu Qiao
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Craig Montell
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, United States
| | - Jia Huang
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
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13
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Li H, Huang CY, Govorunova EG, Sineshchekov OA, Yi A, Rothschild KJ, Wang M, Zheng L, Spudich JL. The crystal structure of bromide-bound GtACR1 reveals a pre-activated state in the transmembrane anion tunnel. eLife 2021; 10:65903. [PMID: 33998458 PMCID: PMC8172240 DOI: 10.7554/elife.65903] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 05/16/2021] [Indexed: 12/16/2022] Open
Abstract
The crystal structure of the light-gated anion channel GtACR1 reported in our previous Research Article (Li et al., 2019) revealed a continuous tunnel traversing the protein from extracellular to intracellular pores. We proposed the tunnel as the conductance channel closed by three constrictions: C1 in the extracellular half, mid-membrane C2 containing the photoactive site, and C3 on the cytoplasmic side. Reported here, the crystal structure of bromide-bound GtACR1 reveals structural changes that relax the C1 and C3 constrictions, including a novel salt-bridge switch mechanism involving C1 and the photoactive site. These findings indicate that substrate binding induces a transition from an inactivated state to a pre-activated state in the dark that facilitates channel opening by reducing free energy in the tunnel constrictions. The results provide direct evidence that the tunnel is the closed form of the channel of GtACR1 and shed light on the light-gated channel activation mechanism.
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Affiliation(s)
- Hai Li
- Department of Biochemistry and Molecular Biology, Center for Membrane Biology, University of Texas Health Science Center - McGovern Medical School, Houston, United States
| | - Chia-Ying Huang
- Swiss Light Source, Paul Scherrer Institute, Villigen, Switzerland
| | - Elena G Govorunova
- Department of Biochemistry and Molecular Biology, Center for Membrane Biology, University of Texas Health Science Center - McGovern Medical School, Houston, United States
| | - Oleg A Sineshchekov
- Department of Biochemistry and Molecular Biology, Center for Membrane Biology, University of Texas Health Science Center - McGovern Medical School, Houston, United States
| | - Adrian Yi
- Molecular Biophysics Laboratory, Photonics Center and Department of Physics, Boston University, Boston, United States
| | - Kenneth J Rothschild
- Molecular Biophysics Laboratory, Photonics Center and Department of Physics, Boston University, Boston, United States
| | - Meitian Wang
- Swiss Light Source, Paul Scherrer Institute, Villigen, Switzerland
| | - Lei Zheng
- Department of Biochemistry and Molecular Biology, Center for Membrane Biology, University of Texas Health Science Center - McGovern Medical School, Houston, United States
| | - John L Spudich
- Department of Biochemistry and Molecular Biology, Center for Membrane Biology, University of Texas Health Science Center - McGovern Medical School, Houston, United States
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14
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Protein Dynamics and Time Resolved Protein Crystallography at Synchrotron Radiation Sources: Past, Present and Future. CRYSTALS 2021. [DOI: 10.3390/cryst11050521] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The ultrabright and ultrashort pulses produced at X-ray free electron lasers (XFELs) has enabled studies of crystallized molecular machines at work under ‘native’ conditions at room temperature by the so-called time-resolved serial femtosecond crystallography (TR-SFX) technique. Since early TR-SFX experiments were conducted at XFELs, it has been largely reported in the literature that time-resolved X-ray experiments at synchrotrons are no longer feasible or are impractical due to the severe technical limitations of these radiation sources. The transfer of the serial crystallography approach to newest synchrotrons upgraded for higher flux density and with beamlines using sophisticated focusing optics, submicron beam diameters and fast low-noise photon-counting detectors offers a way to overcome these difficulties opening new and exciting possibilities. In fact, there is an increasing amount of publications reporting new findings in structural dynamics of protein macromolecules by using time resolved crystallography from microcrystals at synchrotron sources. This review gathers information to provide an overview of the recent work and the advances made in this filed in the past years, as well as outlines future perspectives at the next generation of synchrotron sources and the upcoming compact pulsed X-ray sources.
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15
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Schneider DK, Shi W, Andi B, Jakoncic J, Gao Y, Bhogadi DK, Myers SF, Martins B, Skinner JM, Aishima J, Qian K, Bernstein HJ, Lazo EO, Langdon T, Lara J, Shea-McCarthy G, Idir M, Huang L, Chubar O, Sweet RM, Berman LE, McSweeney S, Fuchs MR. FMX - the Frontier Microfocusing Macromolecular Crystallography Beamline at the National Synchrotron Light Source II. JOURNAL OF SYNCHROTRON RADIATION 2021; 28:650-665. [PMID: 33650577 PMCID: PMC7941291 DOI: 10.1107/s1600577520016173] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 12/11/2020] [Indexed: 05/26/2023]
Abstract
Two new macromolecular crystallography (MX) beamlines at the National Synchrotron Light Source II, FMX and AMX, opened for general user operation in February 2017 [Schneider et al. (2013). J. Phys. Conf. Ser. 425, 012003; Fuchs et al. (2014). J. Phys. Conf. Ser. 493, 012021; Fuchs et al. (2016). AIP Conf. Proc. SRI2015, 1741, 030006]. FMX, the micro-focusing Frontier MX beamline in sector 17-ID-2 at NSLS-II, covers a 5-30 keV photon energy range and delivers a flux of 4.0 × 1012 photons s-1 at 1 Å into a 1 µm × 1.5 µm to 10 µm × 10 µm (V × H) variable focus, expected to reach 5 × 1012 photons s-1 at final storage-ring current. This flux density surpasses most MX beamlines by nearly two orders of magnitude. The high brightness and microbeam capability of FMX are focused on solving difficult crystallographic challenges. The beamline's flexible design supports a wide range of structure determination methods - serial crystallography on micrometre-sized crystals, raster optimization of diffraction from inhomogeneous crystals, high-resolution data collection from large-unit-cell crystals, room-temperature data collection for crystals that are difficult to freeze and for studying conformational dynamics, and fully automated data collection for sample-screening and ligand-binding studies. FMX's high dose rate reduces data collection times for applications like serial crystallography to minutes rather than hours. With associated sample lifetimes as short as a few milliseconds, new rapid sample-delivery methods have been implemented, such as an ultra-high-speed high-precision piezo scanner goniometer [Gao et al. (2018). J. Synchrotron Rad. 25, 1362-1370], new microcrystal-optimized micromesh well sample holders [Guo et al. (2018). IUCrJ, 5, 238-246] and highly viscous media injectors [Weierstall et al. (2014). Nat. Commun. 5, 3309]. The new beamline pushes the frontier of synchrotron crystallography and enables users to determine structures from difficult-to-crystallize targets like membrane proteins, using previously intractable crystals of a few micrometres in size, and to obtain quality structures from irregular larger crystals.
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Affiliation(s)
| | - Wuxian Shi
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Babak Andi
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Jean Jakoncic
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Yuan Gao
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | | | - Stuart F. Myers
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Bruno Martins
- Facility for Rare Isotope Beams, Michigan State University, East Lansing, MI 48824, USA
| | - John M. Skinner
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Jun Aishima
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Kun Qian
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Herbert J. Bernstein
- Ronin Institute for Independent Scholarship, c/o NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Edwin O. Lazo
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Thomas Langdon
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - John Lara
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | | | - Mourad Idir
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Lei Huang
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Oleg Chubar
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Robert M. Sweet
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Lonny E. Berman
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Sean McSweeney
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Martin R. Fuchs
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
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16
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Marlow B, Kuenze G, Li B, Sanders CR, Meiler J. Structural determinants of cholesterol recognition in helical integral membrane proteins. Biophys J 2021; 120:1592-1604. [PMID: 33640379 DOI: 10.1016/j.bpj.2021.02.028] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 01/12/2021] [Accepted: 02/08/2021] [Indexed: 12/20/2022] Open
Abstract
Cholesterol is an integral component of mammalian membranes. It has been shown to modulate membrane fluidity and dynamics and alter integral membrane protein function. However, understanding the molecular mechanisms of how cholesterol impacts protein function is complicated by limited and conflicting structural data. Because of the nature of the crystallization and cryo-EM structure determination, it is difficult to distinguish between specific and biologically relevant interactions and a nonspecific association. The only widely recognized search algorithm for cholesterol-integral-membrane-protein interaction sites is sequence based, i.e., searching for the so-called "Cholesterol Recognition/interaction Amino acid Consensus" motif. Although these motifs are present in numerous integral membrane proteins, there is inconclusive evidence to support their necessity or sufficiency for cholesterol binding. Here, we leverage the increasing number of experimental cholesterol-integral-membrane-protein structures to systematically analyze putative interaction sites based on their spatial arrangement and evolutionary conservation. This analysis creates three-dimensional representations of general cholesterol interaction sites that form clusters across multiple integral membrane protein classes. We also classify cholesterol-integral-membrane-protein interaction sites as either likely-specific or nonspecific. Information gleaned from our characterization will eventually enable a structure-based approach to predict and design cholesterol-integral-membrane-protein interaction sites.
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Affiliation(s)
- Brennica Marlow
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee; Chemical and Physical Biology Program, Vanderbilt University, Nashville, Tennessee
| | - Georg Kuenze
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee; Department of Chemistry, Vanderbilt University, Nashville, Tennessee; Institute for Drug Discovery, Leipzig University Medical School, Leipzig, Germany
| | - Bian Li
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee; Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee
| | - Charles R Sanders
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee; Department of Biochemistry, Vanderbilt University, Nashville, Tennessee
| | - Jens Meiler
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee; Chemical and Physical Biology Program, Vanderbilt University, Nashville, Tennessee; Department of Chemistry, Vanderbilt University, Nashville, Tennessee; Institute for Drug Discovery, Leipzig University Medical School, Leipzig, Germany.
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17
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Recent advances in understanding prodrug transport through the SLC15 family of proton-coupled transporters. Biochem Soc Trans 2021; 48:337-346. [PMID: 32219385 PMCID: PMC7200629 DOI: 10.1042/bst20180302] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 02/15/2020] [Accepted: 03/04/2020] [Indexed: 12/28/2022]
Abstract
Solute carrier (SLC) transporters play important roles in regulating the movement of small molecules and ions across cellular membranes. In mammals, they play an important role in regulating the uptake of nutrients and vitamins from the diet, and in controlling the distribution of their metabolic intermediates within the cell. Several SLC families also play an important role in drug transport and strategies are being developed to hijack SLC transporters to control and regulate drug transport within the body. Through the addition of amino acid and peptide moieties several novel antiviral and anticancer agents have been developed that hijack the proton-coupled oligopeptide transporters, PepT1 (SCL15A1) and PepT2 (SLC15A2), for improved intestinal absorption and renal retention in the body. A major goal is to understand the rationale behind these successes and expand the library of prodrug molecules that utilise SLC transporters. Recent co-crystal structures of prokaryotic homologues of the human PepT1 and PepT2 transporters have shed important new insights into the mechanism of prodrug recognition. Here, I will review recent developments in our understanding of ligand recognition and binding promiscuity within the SLC15 family, and discuss current models for prodrug recognition.
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18
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Renault P, Giraldo J. Dynamical Correlations Reveal Allosteric Sites in G Protein-Coupled Receptors. Int J Mol Sci 2020; 22:ijms22010187. [PMID: 33375427 PMCID: PMC7795036 DOI: 10.3390/ijms22010187] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 12/22/2020] [Accepted: 12/24/2020] [Indexed: 01/14/2023] Open
Abstract
G protein-coupled Receptors (GPCRs) play a central role in many physiological processes and, consequently, constitute important drug targets. In particular, the search for allosteric drugs has recently drawn attention, since they could be more selective and lead to fewer side effects. Accordingly, computational tools have been used to estimate the druggability of allosteric sites in these receptors. In spite of many successful results, the problem is still challenging, particularly the prediction of hydrophobic sites in the interface between the protein and the membrane. In this work, we propose a complementary approach, based on dynamical correlations. Our basic hypothesis was that allosteric sites are strongly coupled to regions of the receptor that undergo important conformational changes upon activation. Therefore, using ensembles of experimental structures, normal mode analysis and molecular dynamics simulations we calculated correlations between internal fluctuations of different sites and a collective variable describing the activation state of the receptor. Then, we ranked the sites based on the strength of their coupling to the collective dynamics. In the β2 adrenergic (β2AR), glucagon (GCGR) and M2 muscarinic receptors, this procedure allowed us to correctly identify known allosteric sites, suggesting it has predictive value. Our results indicate that this dynamics-based approach can be a complementary tool to the existing toolbox to characterize allosteric sites in GPCRs.
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Affiliation(s)
- Pedro Renault
- Laboratory of Molecular Neuropharmacology and Bioinformatics, Unitat de Bioestadística and Institut de Neurociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain;
- Unitat de Neurociència Traslacional, Parc Taulí Hospital Universitari, Institut d’Investigació i Innovació Parc Taulí (I3PT), Institut de Neurociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
- Instituto de Salud Carlos III, Centro de Investigación Biomédica en Red de Salud Mental, CIBERSAM, 08193 Bellaterra, Spain
| | - Jesús Giraldo
- Laboratory of Molecular Neuropharmacology and Bioinformatics, Unitat de Bioestadística and Institut de Neurociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain;
- Unitat de Neurociència Traslacional, Parc Taulí Hospital Universitari, Institut d’Investigació i Innovació Parc Taulí (I3PT), Institut de Neurociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
- Instituto de Salud Carlos III, Centro de Investigación Biomédica en Red de Salud Mental, CIBERSAM, 08193 Bellaterra, Spain
- Correspondence:
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19
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Kilohertz Macromolecular Crystallography Using an EIGER Detector at Low X-ray Fluxes. CRYSTALS 2020. [DOI: 10.3390/cryst10121146] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Time-resolved in-house macromolecular crystallography is primarily limited by the capabilities of the in-house X-ray sources. These sources can only provide a time-averaged structure of the macromolecules. A significant effort has been made in the development of in-house laser-driven ultrafast X-ray sources, with one of the goals as realizing the visualization of the structural dynamics of macromolecules at a very short timescale within the laboratory-scale infrastructure. Most of such in-house ultrafast X-ray sources are operated at high repetition rates and usually deliver very low flux. Therefore, the necessity of a detector that can operate at the repetition rate of the laser and perform extremely well under low flux conditions is essential. Here, we present experimental results demonstrating the usability of the hybrid-pixel detectors, such as Eiger X 1M, and provide experimental proof that they can be successfully operated to collect macromolecular crystallographic data up to a detector frame rate of 3 kHz from synchrotron sources. Our results also show that the data reduction and structural analysis are successful at such high frame rates and fluxes as low as 108 photons/s, which is comparable to the values expected from a typical laser-driven X-ray source.
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20
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Birch J, Cheruvara H, Gamage N, Harrison PJ, Lithgo R, Quigley A. Changes in Membrane Protein Structural Biology. BIOLOGY 2020; 9:E401. [PMID: 33207666 PMCID: PMC7696871 DOI: 10.3390/biology9110401] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/11/2020] [Accepted: 11/12/2020] [Indexed: 12/21/2022]
Abstract
Membrane proteins are essential components of many biochemical processes and are important pharmaceutical targets. Membrane protein structural biology provides the molecular rationale for these biochemical process as well as being a highly useful tool for drug discovery. Unfortunately, membrane protein structural biology is a difficult area of study due to low protein yields and high levels of instability especially when membrane proteins are removed from their native environments. Despite this instability, membrane protein structural biology has made great leaps over the last fifteen years. Today, the landscape is almost unrecognisable. The numbers of available atomic resolution structures have increased 10-fold though advances in crystallography and more recently by cryo-electron microscopy. These advances in structural biology were achieved through the efforts of many researchers around the world as well as initiatives such as the Membrane Protein Laboratory (MPL) at Diamond Light Source. The MPL has helped, provided access to and contributed to advances in protein production, sample preparation and data collection. Together, these advances have enabled higher resolution structures, from less material, at a greater rate, from a more diverse range of membrane protein targets. Despite this success, significant challenges remain. Here, we review the progress made and highlight current and future challenges that will be overcome.
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Affiliation(s)
- James Birch
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Harish Cheruvara
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Nadisha Gamage
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Peter J. Harrison
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Ryan Lithgo
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, Leicestershire, UK
| | - Andrew Quigley
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
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21
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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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22
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Martiel I, Huang CY, Villanueva-Perez P, Panepucci E, Basu S, Caffrey M, Pedrini B, Bunk O, Stampanoni M, Wang M. Low-dose in situ prelocation of protein microcrystals by 2D X-ray phase-contrast imaging for serial crystallography. IUCRJ 2020; 7:1131-1141. [PMID: 33209324 PMCID: PMC7642777 DOI: 10.1107/s2052252520013238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/01/2020] [Indexed: 06/11/2023]
Abstract
Serial protein crystallography has emerged as a powerful method of data collection on small crystals from challenging targets, such as membrane proteins. Multiple microcrystals need to be located on large and often flat mounts while exposing them to an X-ray dose that is as low as possible. A crystal-prelocation method is demonstrated here using low-dose 2D full-field propagation-based X-ray phase-contrast imaging at the X-ray imaging beamline TOMCAT at the Swiss Light Source (SLS). This imaging step provides microcrystal coordinates for automated serial data collection at a microfocus macromolecular crystallography beamline on samples with an essentially flat geometry. This prelocation method was applied to microcrystals of a soluble protein and a membrane protein, grown in a commonly used double-sandwich in situ crystallization plate. The inner sandwiches of thin plastic film enclosing the microcrystals in lipid cubic phase were flash cooled and imaged at TOMCAT. Based on the obtained crystal coordinates, both still and rotation wedge serial data were collected automatically at the SLS PXI beamline, yielding in both cases a high indexing rate. This workflow can be easily implemented at many synchrotron facilities using existing equipment, or potentially integrated as an online technique in the next-generation macromolecular crystallography beamline, and thus benefit a number of dose-sensitive challenging protein targets.
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Affiliation(s)
- Isabelle Martiel
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen, 5232, Switzerland
| | - Chia-Ying Huang
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen, 5232, Switzerland
| | - Pablo Villanueva-Perez
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen, 5232, Switzerland
- Synchrotron Radiation Research and NanoLund, Lund University, Box 118, Lund, 221 00, Sweden
| | - Ezequiel Panepucci
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen, 5232, Switzerland
| | - Shibom Basu
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen, 5232, Switzerland
- EMBL Grenoble, 71 avenue des Martyrs, Grenoble, 38042, France
| | - Martin Caffrey
- School of Medicine and School of Biochemistry and Immunology, Trinity College, Dublin 2, D02 R590, Ireland
| | - Bill Pedrini
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen, 5232, Switzerland
| | - Oliver Bunk
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen, 5232, Switzerland
| | - Marco Stampanoni
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen, 5232, Switzerland
- Institute of Biomedical Engineering, University and ETH Zurich, Zurich, 8092, Switzerland
| | - Meitian Wang
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen, 5232, Switzerland
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Lasitza‐Male T, Bartels K, Jungwirth J, Wiggers F, Rosenblum G, Hofmann H, Löw C. Membrane Chemistry Tunes the Structure of a Peptide Transporter. Angew Chem Int Ed Engl 2020; 59:19121-19128. [PMID: 32744783 PMCID: PMC7590137 DOI: 10.1002/anie.202008226] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Indexed: 01/02/2023]
Abstract
Membrane proteins require lipid bilayers for function. While lipid compositions reach enormous complexities, high-resolution structures are usually obtained in artificial detergents. To understand whether and how lipids guide membrane protein function, we use single-molecule FRET to probe the dynamics of DtpA, a member of the proton-coupled oligopeptide transporter (POT) family, in various lipid environments. We show that detergents trap DtpA in a dynamic ensemble with cytoplasmic opening. Only reconstitutions in more native environments restore cooperativity, allowing an opening to the extracellular side and a sampling of all relevant states. Bilayer compositions tune the abundance of these states. A novel state with an extreme cytoplasmic opening is accessible in bilayers with anionic head groups. Hence, chemical diversity of membranes translates into structural diversity, with the current POT structures only sampling a portion of the full structural space.
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Affiliation(s)
- Tanya Lasitza‐Male
- Department of Structural BiologyWeizmann Institute of ScienceHerzl St. 2347610001RehovotIsrael
| | - Kim Bartels
- Centre for Structural Systems Biology (CSSB)DESY and European Molecular Biology Laboratory HamburgNotkestrasse 8522607HamburgGermany
| | - Jakub Jungwirth
- Department of Chemical and Biological PhysicsWeizmann Institute of ScienceHerzl St. 2347610001RehovotIsrael
| | - Felix Wiggers
- Department of Structural BiologyWeizmann Institute of ScienceHerzl St. 2347610001RehovotIsrael
| | - Gabriel Rosenblum
- Department of Structural BiologyWeizmann Institute of ScienceHerzl St. 2347610001RehovotIsrael
| | - Hagen Hofmann
- Department of Structural BiologyWeizmann Institute of ScienceHerzl St. 2347610001RehovotIsrael
| | - Christian Löw
- Centre for Structural Systems Biology (CSSB)DESY and European Molecular Biology Laboratory HamburgNotkestrasse 8522607HamburgGermany
- Department of Medical Biochemistry and BiophysicsKarolinska Institutet17177StockholmSweden
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24
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Lasitza‐Male T, Bartels K, Jungwirth J, Wiggers F, Rosenblum G, Hofmann H, Löw C. Membrane Chemistry Tunes the Structure of a Peptide Transporter. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202008226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Tanya Lasitza‐Male
- Department of Structural Biology Weizmann Institute of Science Herzl St. 234 7610001 Rehovot Israel
| | - Kim Bartels
- Centre for Structural Systems Biology (CSSB) DESY and European Molecular Biology Laboratory Hamburg Notkestrasse 85 22607 Hamburg Germany
| | - Jakub Jungwirth
- Department of Chemical and Biological Physics Weizmann Institute of Science Herzl St. 234 7610001 Rehovot Israel
| | - Felix Wiggers
- Department of Structural Biology Weizmann Institute of Science Herzl St. 234 7610001 Rehovot Israel
| | - Gabriel Rosenblum
- Department of Structural Biology Weizmann Institute of Science Herzl St. 234 7610001 Rehovot Israel
| | - Hagen Hofmann
- Department of Structural Biology Weizmann Institute of Science Herzl St. 234 7610001 Rehovot Israel
| | - Christian Löw
- Centre for Structural Systems Biology (CSSB) DESY and European Molecular Biology Laboratory Hamburg Notkestrasse 85 22607 Hamburg Germany
- Department of Medical Biochemistry and Biophysics Karolinska Institutet 17177 Stockholm Sweden
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25
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Jastrzębski S, Szymczak M, Pocha A, Mordalski S, Tabor J, Bojarski AJ, Podlewska S. Emulating Docking Results Using a Deep Neural Network: A New Perspective for Virtual Screening. J Chem Inf Model 2020; 60:4246-4262. [DOI: 10.1021/acs.jcim.9b01202] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Stanisław Jastrzębski
- Faculty of Mathematics and Computer Science, Jagiellonian University, 6 Łojasiewicza Street, 30-348 Kraków, Poland
| | - Maciej Szymczak
- Faculty of Mathematics and Computer Science, Jagiellonian University, 6 Łojasiewicza Street, 30-348 Kraków, Poland
| | - Agnieszka Pocha
- Faculty of Mathematics and Computer Science, Jagiellonian University, 6 Łojasiewicza Street, 30-348 Kraków, Poland
| | - Stefan Mordalski
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
- Maj Institute of Pharmacology, Polish Academy of Sciences, 12 Smętna Street, 31-343 Kraków, Poland
| | - Jacek Tabor
- Faculty of Mathematics and Computer Science, Jagiellonian University, 6 Łojasiewicza Street, 30-348 Kraków, Poland
| | - Andrzej J. Bojarski
- Maj Institute of Pharmacology, Polish Academy of Sciences, 12 Smętna Street, 31-343 Kraków, Poland
| | - Sabina Podlewska
- Maj Institute of Pharmacology, Polish Academy of Sciences, 12 Smętna Street, 31-343 Kraków, Poland
- Department of Technology and Biotechnology of Drugs, Jagiellonian University Medical College, 9 Medyczna Street, 30-688 Kraków, Poland
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26
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Design, Synthesis, and Evaluation of X-ray Crystal Structure, Biological Activities, DFT Calculations, and Molecular Docking of Phenyl Imidazolidin-2-One Derivatives. CRYSTALS 2020. [DOI: 10.3390/cryst10080713] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Eight phenyl imidazolinone derivatives were synthesized from N2-(2,4-dimethylphenyl)-N1-methyformamidine (DPMF) via scaffold-hopping method using the ring-closure approach. The prepared compounds were verified using 1H and 13C NMR and HRMS spectroscopies. The structure of compound 3c was confirmed by single-crystal X-ray diffraction analysis. The mean plane of the phenyl and imidazolinone moieties was almost coplanar with an angle of 8.85(4)°. In the crystal, molecules were interlinked with intermolecular hydrogen bonds (N–H···O and C–H···O), generating a network structure. Additionally, compound 3f displayed the highest insecticidal activity (86.7%) against Plutella xylostella at 600 mg/L, which was significantly higher than the insecticidal activity (23.0%) of DPMF. Also, compound 3d displayed good fungicidal activities against Phytophthora capsici, Phytophthora sojae, and Phytophthora infestans. Density functional theory (DFT) calculations were performed to explain the insecticidal and fungicidal activities of phenyl imidazolidin-2-one derivatives, especially potent compounds 3f and 3d. Moreover, the binding modes of compounds 3a–h and DPMF against octopamine receptor of Plutella xylostella were studied by homology modeling and molecular docking. Therefore, a preliminary structure–activity relationship (SAR) was derived and discussed. These results encourage the exploration of novel insecticides and fungicides based on DPMF.
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Lawrence JM, Orlans J, Evans G, Orville AM, Foadi J, Aller P. High-throughput in situ experimental phasing. Acta Crystallogr D Struct Biol 2020; 76:790-801. [PMID: 32744261 PMCID: PMC7397491 DOI: 10.1107/s2059798320009109] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 07/03/2020] [Indexed: 11/10/2022] Open
Abstract
In this article, a new approach to experimental phasing for macromolecular crystallography (MX) at synchrotrons is introduced and described for the first time. It makes use of automated robotics applied to a multi-crystal framework in which human intervention is reduced to a minimum. Hundreds of samples are automatically soaked in heavy-atom solutions, using a Labcyte Inc. Echo 550 Liquid Handler, in a highly controlled and optimized fashion in order to generate derivatized and isomorphous crystals. Partial data sets obtained on MX beamlines using an in situ setup for data collection are processed with the aim of producing good-quality anomalous signal leading to successful experimental phasing.
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Affiliation(s)
- Joshua M. Lawrence
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Julien Orlans
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- UMR0203, Biologie Fonctionnelle, Insectes et Interactions (BF2i); Institut National des Sciences Appliquées de Lyon (INSA Lyon); Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Lyon (Univ Lyon), F-69621 Villeurbanne, France
| | - Gwyndaf Evans
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Allen M. Orville
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
| | - James Foadi
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Pierre Aller
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
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28
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Huang CY, Meier N, Caffrey M, Wang M, Olieric V. 3D-printed holders for in meso in situ fixed-target serial X-ray crystallography. J Appl Crystallogr 2020; 53:854-859. [PMID: 32684901 PMCID: PMC7312129 DOI: 10.1107/s1600576720002897] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 03/01/2020] [Indexed: 11/10/2022] Open
Abstract
The in meso in situ serial X-ray crystallography method was developed to ease the handling of small fragile crystals of membrane proteins and for rapid data collection on hundreds of microcrystals directly in the growth medium without the need for crystal harvesting. To facilitate mounting of these in situ samples on a goniometer at cryogenic or at room temperatures, two new 3D-printed holders have been developed. They provide for cubic and sponge phase sample stability in the X-ray beam and are compatible with sample-changing robots. The holders can accommodate a variety of window material types, as well as bespoke samples for diffraction screening and data collection at conventional macromolecular crystallography beamlines. They can be used for convenient post-crystallization treatments such as ligand and heavy-atom soaking. The design, assembly and application of the holders for in situ serial crystallography are described. Files for making the holders using a 3D printer are included as supporting information.
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Affiliation(s)
- Chia-Ying Huang
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen-PSI, 5232, Switzerland
| | - Nathalie Meier
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen-PSI, 5232, Switzerland
| | - Martin Caffrey
- Membrane Structural and Functional Biology Group, Trinity Biomedical Sciences Institute, Trinity College, Dublin 2, D02 R590, Ireland
| | - Meitian Wang
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen-PSI, 5232, Switzerland
| | - Vincent Olieric
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen-PSI, 5232, Switzerland
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Martiel I, Mozzanica A, Opara NL, Panepucci E, Leonarski F, Redford S, Mohacsi I, Guzenko V, Ozerov D, Padeste C, Schmitt B, Pedrini B, Wang M. X-ray fluorescence detection for serial macromolecular crystallography using a JUNGFRAU pixel detector. JOURNAL OF SYNCHROTRON RADIATION 2020; 27:329-339. [PMID: 32153271 PMCID: PMC7064105 DOI: 10.1107/s1600577519016758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 12/14/2019] [Indexed: 05/06/2023]
Abstract
Detection of heavy elements, such as metals, in macromolecular crystallography (MX) samples by X-ray fluorescence is a function traditionally covered at synchrotron MX beamlines by silicon drift detectors, which cannot be used at X-ray free-electron lasers because of the very short duration of the X-ray pulses. Here it is shown that the hybrid pixel charge-integrating detector JUNGFRAU can fulfill this function when operating in a low-flux regime. The feasibility of precise position determination of micrometre-sized metal marks is also demonstrated, to be used as fiducials for offline prelocation in serial crystallography experiments, based on the specific fluorescence signal measured with JUNGFRAU, both at the synchrotron and at SwissFEL. Finally, the measurement of elemental absorption edges at a synchrotron beamline using JUNGFRAU is also demonstrated.
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Affiliation(s)
- Isabelle Martiel
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen 5232, Switzerland
| | - Aldo Mozzanica
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen 5232, Switzerland
| | - Nadia L. Opara
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen 5232, Switzerland
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Basel 4058, Switzerland
- SwissNanoscience Institute, University of Basel, Basel 4056, Switzerland
| | - Ezequiel Panepucci
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen 5232, Switzerland
| | - Filip Leonarski
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen 5232, Switzerland
| | - Sophie Redford
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen 5232, Switzerland
| | - Istvan Mohacsi
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen 5232, Switzerland
| | - Vitaliy Guzenko
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen 5232, Switzerland
| | - Dmitry Ozerov
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen 5232, Switzerland
| | - Celestino Padeste
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen 5232, Switzerland
| | - Bernd Schmitt
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen 5232, Switzerland
| | - Bill Pedrini
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen 5232, Switzerland
| | - Meitian Wang
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen 5232, Switzerland
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30
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Structure and Functional Characterization of Membrane Integral Proteins in the Lipid Cubic Phase. J Mol Biol 2020; 432:5104-5123. [PMID: 32113953 DOI: 10.1016/j.jmb.2020.02.024] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Revised: 02/14/2020] [Accepted: 02/19/2020] [Indexed: 12/19/2022]
Abstract
The lipid cubic phase (LCP) has been used extensively as a medium for crystallizing membrane proteins. It is an attractive environment in which to perform such studies because it incorporates a lipid bilayer. It is therefore considered a useful and a faithful biomembrane mimetic. Here, we bring together evidence that supports this view. Biophysical characterizations are described demonstrating that the cubic phase is a porous medium into and out of which water-soluble molecules can diffuse for binding to and reaction with reconstituted proteins. The proteins themselves are shown to be functionally reconstituted into and to have full mobility in the bilayered membrane, a prerequisite for LCP crystallogenesis. Spectroscopic methods have been used to characterize the conformation and disposition of proteins in the mesophase. Procedures for performing activity assays on enzymes directly in the cubic phase have been reported. Specific examples described here include a kinase and two transferases, where quantitative kinetics and mechanism-defining measurements were performed directly or via a coupled assay system. Finally, ligand-binding assays are described, where binding to proteins in the mesophase membrane was monitored directly by eye and indirectly by fluorescence quenching, enabling binding constant determinations for targets with affinity values in the micromolar and nanomolar range. These results make a convincing case that the lipid bilayer of the cubic mesophase is an excellent membrane mimetic and a suitable medium in which to perform not only crystallogenesis but also biochemical and biophysical characterizations of membrane proteins.
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31
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Huang CY, Olieric V, Caffrey M, Wang M. In Meso In Situ Serial X-Ray Crystallography (IMISX): A Protocol for Membrane Protein Structure Determination at the Swiss Light Source. Methods Mol Biol 2020; 2127:293-319. [PMID: 32112330 DOI: 10.1007/978-1-0716-0373-4_20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The lipid cubic phases (LCP) have enabled the determination of many important high-resolution structures of membrane proteins such as G-protein-coupled receptors, photosensitive proteins, enzymes, channels, and transporters. However, harvesting the crystals from the glass or plastic plates in which crystals grow is challenging. The in meso in situ serial X-ray crystallography (IMISX) method uses thin plastic windowed plates that minimize LCP crystal manipulation. The method, which is compatible with high-throughput in situ measurements, allows systematic diffraction screening and rapid data collection from hundreds of microcrystals in in meso crystallization wells without direct crystal harvesting. In this chapter, we describe an IMISX protocol for in situ serial X-ray data collection of LCP-grown crystals at both cryogenic and room temperatures which includes the crystallization setup, sample delivery, automated serial diffraction data collection, and experimental phasing. We also detail how the IMISX method was applied successfully for the structure determination of two novel targets-the undecaprenyl-pyrophosphate phosphatase BacA and the chemokine G-protein-coupled receptor CCR2A.
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Affiliation(s)
- Chia-Ying Huang
- Swiss Light Source, Paul Scherrer Institut, Forschungsstrasse 111, Villigen-PSI, 5232, Switzerland.
| | - Vincent Olieric
- Swiss Light Source, Paul Scherrer Institut, Forschungsstrasse 111, Villigen-PSI, 5232, Switzerland
| | - Martin Caffrey
- Membrane Structural and Functional Biology (MS&FB) Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland
| | - Meitian Wang
- Swiss Light Source, Paul Scherrer Institut, Forschungsstrasse 111, Villigen-PSI, 5232, Switzerland
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32
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Abstract
Asthma is a heterogeneous inflammatory disease of the airways that is associated with airway hyperresponsiveness and airflow limitation. Although asthma was once simply categorized as atopic or nonatopic, emerging analyses over the last few decades have revealed a variety of asthma endotypes that are attributed to numerous pathophysiological mechanisms. The classification of asthma by endotype is primarily routed in different profiles of airway inflammation that contribute to bronchoconstriction. Many asthma therapeutics target G protein-coupled receptors (GPCRs), which either enhance bronchodilation or prevent bronchoconstriction. Short-acting and long-acting β 2-agonists are widely used bronchodilators that signal through the activation of the β 2-adrenergic receptor. Short-acting and long-acting antagonists of muscarinic acetylcholine receptors are used to reduce bronchoconstriction by blocking the action of acetylcholine. Leukotriene antagonists that block the signaling of cysteinyl leukotriene receptor 1 are used as an add-on therapy to reduce bronchoconstriction and inflammation induced by cysteinyl leukotrienes. A number of GPCR-targeting asthma drug candidates are also in different stages of development. Among them, antagonists of prostaglandin D2 receptor 2 have advanced into phase III clinical trials. Others, including antagonists of the adenosine A2B receptor and the histamine H4 receptor, are in early stages of clinical investigation. In the past decade, significant research advancements in pharmacology, cell biology, structural biology, and molecular physiology have greatly deepened our understanding of the therapeutic roles of GPCRs in asthma and drug action on these GPCRs. This review summarizes our current understanding of GPCR signaling and pharmacology in the context of asthma treatment. SIGNIFICANCE STATEMENT: Although current treatment methods for asthma are effective for a majority of asthma patients, there are still a large number of patients with poorly controlled asthma who may experience asthma exacerbations. This review summarizes current asthma treatment methods and our understanding of signaling and pharmacology of G protein-coupled receptors (GPCRs) in asthma therapy, and discusses controversies regarding the use of GPCR drugs and new opportunities in developing GPCR-targeting therapeutics for the treatment of asthma.
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Affiliation(s)
- Stacy Gelhaus Wendell
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania (S.G.W., C.Z.); Bioinformatics Institute, Agency for Science, Technology, and Research, Singapore (H.F.); and Department of Biological Sciences, National University of Singapore, and Center for Computational Biology, DUKE-NUS Medical School, Singapore (H.F.)
| | - Hao Fan
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania (S.G.W., C.Z.); Bioinformatics Institute, Agency for Science, Technology, and Research, Singapore (H.F.); and Department of Biological Sciences, National University of Singapore, and Center for Computational Biology, DUKE-NUS Medical School, Singapore (H.F.)
| | - Cheng Zhang
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania (S.G.W., C.Z.); Bioinformatics Institute, Agency for Science, Technology, and Research, Singapore (H.F.); and Department of Biological Sciences, National University of Singapore, and Center for Computational Biology, DUKE-NUS Medical School, Singapore (H.F.)
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Abdulganiyyu IA, Sani MA, Separovic F, Marco H, Jackson GE. Phote-HrTH (Phormia terraenovae Hypertrehalosaemic Hormone), the Metabolic Hormone of the Fruit Fly: Solution Structure and Receptor Binding Model. Aust J Chem 2020. [DOI: 10.1071/ch19461] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Fruit flies are a widely distributed pest insect that pose a significant threat to food security. Flight is essential for the dispersal of the adult flies to find new food sources and ideal breeding spots. The supply of metabolic fuel to power the flight muscles of insects is regulated by adipokinetic hormones (AKHs). The fruit fly, Drosophila melanogaster, has the same AKH that is present in the blowfly, Phormia terraenovae; this AKH has the code-name Phote-HrTH. Binding of the AKH to the extra-cellular binding site of a G protein-coupled receptor causes its activation. In this paper, the structure of Phote-HrTH in sodium dodecyl sulfate (SDS) micelle solution was determined using NMR restrained molecular dynamics. The peptide was found to bind to the micelle and be fairly rigid, with an S2 order parameter of 0.96. The translated protein sequence of the AKH receptor from the fruit fly, D. melanogaster, Drome-AKHR, was used to construct two models of the receptor. It is proposed that these two models represent the active and inactive state of the receptor. The model based on the crystal structure of the β-2 adrenergic receptor was found to bind Phote-HrTH with a binding constant of −102kJmol−1, while the other model, based on the crystal structure of rhodopsin, did not bind the peptide. Under molecular dynamic simulation, in a palmitoyloleoylphosphatidylcholine (POPC) membrane, the receptor complex changed from an inactive to an active state. The identification and characterisation of the ligand binding site of Drome-AKHR provide novel information of ligand–receptor interaction, which could lead to the development of species-specific control substances to use discriminately against the fruit fly.
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34
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Cheng R, Huang C, Hennig M, Nar H, Schnapp G. In situ
crystallography as an emerging method for structure solution of membrane proteins: the case of CCR2A. FEBS J 2019; 287:866-873. [DOI: 10.1111/febs.15098] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 09/10/2019] [Accepted: 10/15/2019] [Indexed: 12/27/2022]
Affiliation(s)
| | - Chia‐Ying Huang
- Swiss Light Source Paul Scherrer Institute Villigen Switzerland
| | | | - Herbert Nar
- Boehringer Ingelheim Pharma GmbH & Co. KG Biberach Germany
| | - Gisela Schnapp
- Boehringer Ingelheim Pharma GmbH & Co. KG Biberach Germany
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35
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Zhang W, Wu H, Zhang R, Fang X, Xu W. Structure and effective charge characterization of proteins by a mobility capillary electrophoresis based method. Chem Sci 2019; 10:7779-7787. [PMID: 31588326 PMCID: PMC6761862 DOI: 10.1039/c9sc02039j] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 07/02/2019] [Indexed: 12/18/2022] Open
Abstract
Measuring the conformations and effective charges of proteins in solution is critical for investigating protein bioactivity, but their rapid analysis remains a challenging problem. Here we report a mobility capillary electrophoresis (MCE) based method for the rapid analysis of protein stereo-structures and effective charges in different solution environments. With the capability of mixture separation, MCE measures the hydrodynamic radius of a protein through Taylor dispersion analysis and its effective charge through ion mobility analysis. The experimental results acquired from MCE are then utilized to restrain molecular dynamics simulations, so that the most probable conformation of that protein can be obtained. As proof-of-concept demonstrations, the charge states and structures of five proteins were analyzed under close to native environments. The conformation transitions and charge state variations of bovine serum albumin and lysozyme under different pH conditions were also investigated. This method is promising for high-throughput protein analysis, which could potentially be coupled with mass spectrometry for investigating protein stereo-structures and functions in top-down proteomics.
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Affiliation(s)
- Wenjing Zhang
- School of Life Science , Beijing Institute of Technology , No. 5 South Zhongguancun Street, Haidian Dist , Beijing , China .
| | - Haimei Wu
- School of Life Science , Beijing Institute of Technology , No. 5 South Zhongguancun Street, Haidian Dist , Beijing , China .
| | - Rongkai Zhang
- School of Life Science , Beijing Institute of Technology , No. 5 South Zhongguancun Street, Haidian Dist , Beijing , China .
| | - Xiang Fang
- National Institute of Metrology , No. 18, Bei San Huan Dong Lu, Chaoyang Dist , Beijing , China
| | - Wei Xu
- School of Life Science , Beijing Institute of Technology , No. 5 South Zhongguancun Street, Haidian Dist , Beijing , China .
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36
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Förster A, Brandstetter S, Schulze-Briese C. Transforming X-ray detection with hybrid photon counting detectors. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2019; 377:20180241. [PMID: 31030653 PMCID: PMC6501887 DOI: 10.1098/rsta.2018.0241] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/27/2019] [Indexed: 05/22/2023]
Abstract
Hybrid photon counting (HPC) detectors have radically transformed basic research at synchrotron light sources since 2006. They excel at X-ray diffraction applications in the energy range from 2 to 100 keV. The main reasons for their superiority are the direct detection of individual photons and the accurate determination of scattering and diffraction intensities over an extremely high dynamic range. The detectors were first adopted in macromolecular crystallography where they revolutionized data collection. They were soon also used for small-angle scattering, coherent scattering, powder X-ray diffraction, spectroscopy and increasingly high-energy applications. Here, we will briefly survey the history of HPC detectors, explain their technology and then show in detail how improved detection has transformed a wide range of experimental techniques. We will end with an outlook to the future, which will probably see HPC technology find even broader use, for example, in electron microscopy and medical applications. This article is part of the theme issue 'Fifty years of synchrotron science: achievements and opportunities'.
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37
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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 PMCID: PMC6628340 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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38
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Basu S, Olieric V, Leonarski F, Matsugaki N, Kawano Y, Takashi T, Huang CY, Yamada Y, Vera L, Olieric N, Basquin J, Wojdyla JA, Bunk O, Diederichs K, Yamamoto M, Wang M. Long-wavelength native-SAD phasing: opportunities and challenges. IUCRJ 2019; 6:373-386. [PMID: 31098019 PMCID: PMC6503925 DOI: 10.1107/s2052252519002756] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 02/22/2019] [Indexed: 05/04/2023]
Abstract
Native single-wavelength anomalous dispersion (SAD) is an attractive experimental phasing technique as it exploits weak anomalous signals from intrinsic light scatterers (Z < 20). The anomalous signal of sulfur in particular, is enhanced at long wavelengths, however the absorption of diffracted X-rays owing to the crystal, the sample support and air affects the recorded intensities. Thereby, the optimal measurable anomalous signals primarily depend on the counterplay of the absorption and the anomalous scattering factor at a given X-ray wavelength. Here, the benefit of using a wavelength of 2.7 over 1.9 Å is demonstrated for native-SAD phasing on a 266 kDa multiprotein-ligand tubulin complex (T2R-TTL) and is applied in the structure determination of an 86 kDa helicase Sen1 protein at beamline BL-1A of the KEK Photon Factory, Japan. Furthermore, X-ray absorption at long wavelengths was controlled by shaping a lysozyme crystal into spheres of defined thicknesses using a deep-UV laser, and a systematic comparison between wavelengths of 2.7 and 3.3 Å is reported for native SAD. The potential of laser-shaping technology and other challenges for an optimized native-SAD experiment at wavelengths >3 Å are discussed.
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Affiliation(s)
- Shibom Basu
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
| | - Vincent Olieric
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
| | - Filip Leonarski
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
| | - Naohiro Matsugaki
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, Tsukuba, 305-0801, Japan
| | - Yoshiaki Kawano
- Advanced Photon Technology Division, RIKEN SPring-8 Center, Hyogo 679-5148, Japan
| | - Tomizaki Takashi
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
| | - Chia-Ying Huang
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
| | - Yusuke Yamada
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, Tsukuba, 305-0801, Japan
| | - Laura Vera
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
| | - Natacha Olieric
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institut, Villigen, PSI 5232, Switzerland
| | - Jerome Basquin
- Department of Biochemistry, Max Planck Institute of Biochemistry, Munich, Germany
| | - Justyna A. Wojdyla
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
| | - Oliver Bunk
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
| | - Kay Diederichs
- Department of Biology, University of Konstanz, Konstanz, 78457, Germany
| | - Masaki Yamamoto
- Advanced Photon Technology Division, RIKEN SPring-8 Center, Hyogo 679-5148, Japan
| | - Meitian Wang
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
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39
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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: 30] [Impact Index Per Article: 6.0] [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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40
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Basu S, Finke A, Vera L, Wang M, Olieric V. Making routine native SAD a reality: lessons from beamline X06DA at the Swiss Light Source. Acta Crystallogr D Struct Biol 2019; 75:262-271. [PMID: 30950397 PMCID: PMC6450063 DOI: 10.1107/s2059798319003103] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 03/01/2019] [Indexed: 01/19/2023] Open
Abstract
Native single-wavelength anomalous dispersion (SAD) is the most attractive de novo phasing method in macromolecular crystallography, as it directly utilizes intrinsic anomalous scattering from native crystals. However, the success of such an experiment depends on accurate measurements of the reflection intensities and therefore on careful data-collection protocols. Here, the low-dose, multiple-orientation data-collection protocol for native SAD phasing developed at beamline X06DA (PXIII) at the Swiss Light Source is reviewed, and its usage over the last four years on conventional crystals (>50 µm) is reported. Being experimentally very simple and fast, this method has gained popularity and has delivered 45 de novo structures to date (13 of which have been published). Native SAD is currently the primary choice for experimental phasing among X06DA users. The method can address challenging cases: here, native SAD phasing performed on a streptavidin-biotin crystal with P21 symmetry and a low Bijvoet ratio of 0.6% is highlighted. The use of intrinsic anomalous signals as sequence markers for model building and the assignment of ions is also briefly described.
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Affiliation(s)
- Shibom Basu
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - Aaron Finke
- MacCHESS, Cornell University, Ithaca, New York, USA
| | - Laura Vera
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - Meitian Wang
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - Vincent Olieric
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, Switzerland
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41
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Wierman JL, Paré-Labrosse O, Sarracini A, Besaw JE, Cook MJ, Oghbaey S, Daoud H, Mehrabi P, Kriksunov I, Kuo A, Schuller DJ, Smith S, Ernst OP, Szebenyi DME, Gruner SM, Miller RJD, Finke AD. Fixed-target serial oscillation crystallography at room temperature. IUCRJ 2019; 6:305-316. [PMID: 30867928 PMCID: PMC6400179 DOI: 10.1107/s2052252519001453] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Accepted: 01/25/2019] [Indexed: 05/18/2023]
Abstract
A fixed-target approach to high-throughput room-temperature serial synchrotron crystallography with oscillation is described. Patterned silicon chips with microwells provide high crystal-loading density with an extremely high hit rate. The microfocus, undulator-fed beamline at CHESS, which has compound refractive optics and a fast-framing detector, was built and optimized for this experiment. The high-throughput oscillation method described here collects 1-5° of data per crystal at room temperature with fast (10° s-1) oscillation rates and translation times, giving a crystal-data collection rate of 2.5 Hz. Partial datasets collected by the oscillation method at a storage-ring source provide more complete data per crystal than still images, dramatically lowering the total number of crystals needed for a complete dataset suitable for structure solution and refinement - up to two orders of magnitude fewer being required. Thus, this method is particularly well suited to instances where crystal quantities are low. It is demonstrated, through comparison of first and last oscillation images of two systems, that dose and the effects of radiation damage can be minimized through fast rotation and low angular sweeps for each crystal.
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Affiliation(s)
| | - Olivier Paré-Labrosse
- Departments of Chemistry and Physics, University of Toronto, Toronto, ON Canada
- Max Planck Institute for the Structure and Dynamics of Matter, Hamburg, Germany
| | - Antoine Sarracini
- Departments of Chemistry and Physics, University of Toronto, Toronto, ON Canada
| | - Jessica E. Besaw
- Departments of Chemistry and Physics, University of Toronto, Toronto, ON Canada
| | | | - Saeed Oghbaey
- Departments of Chemistry and Physics, University of Toronto, Toronto, ON Canada
| | - Hazem Daoud
- Departments of Chemistry and Physics, University of Toronto, Toronto, ON Canada
| | - Pedram Mehrabi
- Max Planck Institute for the Structure and Dynamics of Matter, Hamburg, Germany
| | | | - Anling Kuo
- Departments of Biochemistry and Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | - Scott Smith
- MacCHESS, Cornell University, Ithaca, NY 14853, USA
| | - Oliver P. Ernst
- Departments of Biochemistry and Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | - Sol M. Gruner
- MacCHESS, Cornell University, Ithaca, NY 14853, USA
- Department of Physics, Cornell University, Ithaca, NY 14853, USA
- Kavli Institute for Nanoscale Science, Cornell University, Ithaca, NY 14853, USA
| | - R. J. Dwayne Miller
- Departments of Chemistry and Physics, University of Toronto, Toronto, ON Canada
- Max Planck Institute for the Structure and Dynamics of Matter, Hamburg, Germany
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42
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Behrens M, Briand L, de March CA, Matsunami H, Yamashita A, Meyerhof W, Weyand S. Structure-Function Relationships of Olfactory and Taste Receptors. Chem Senses 2019; 43:81-87. [PMID: 29342245 DOI: 10.1093/chemse/bjx083] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The field of chemical senses has made major progress in understanding the cellular mechanisms of olfaction and taste in the past 2 decades. However, the molecular understanding of odor and taste recognition is still lagging far behind and will require solving multiple structures of the relevant full-length receptors in complex with native ligands to achieve this goal. However, the development of multiple complimentary strategies for the structure determination of G protein-coupled receptors (GPCRs) makes this goal realistic. The common conundrum of how multi-specific receptors that recognize a large number of different ligands results in a sensory perception in the brain will only be fully understood by a combination of high-resolution receptor structures and functional studies. This review discusses the first steps on this pathway, including biochemical and physiological assays, forward genetics approaches, molecular modeling, and the first steps towards the structural biology of olfactory and taste receptors.
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Affiliation(s)
- Maik Behrens
- Department of Molecular Genetics, German Institute of Human Nutrition Potsdam-Rehbruecke, Germany
| | - Loïc Briand
- Centre des Sciences du Goût et de l'Alimentation, AgroSup Dijon, CNRS, INRA, Univ. de Bourgogne- Franche-Comté, France
| | - Claire A de March
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, USA
| | - Hiroaki Matsunami
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, USA
| | - Atsuko Yamashita
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Japan
| | - Wolfgang Meyerhof
- Department of Molecular Genetics, German Institute of Human Nutrition Potsdam-Rehbruecke, Germany
| | - Simone Weyand
- Department of Biochemistry, University of Cambridge, UK
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43
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Basu S, Kaminski JW, Panepucci E, Huang CY, Warshamanage R, Wang M, Wojdyla JA. Automated data collection and real-time data analysis suite for serial synchrotron crystallography. JOURNAL OF SYNCHROTRON RADIATION 2019; 26:244-252. [PMID: 30655492 PMCID: PMC6337882 DOI: 10.1107/s1600577518016570] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 11/21/2018] [Indexed: 05/03/2023]
Abstract
At the Swiss Light Source macromolecular crystallography (MX) beamlines the collection of serial synchrotron crystallography (SSX) diffraction data is facilitated by the recent DA+ data acquisition and analysis software developments. The SSX suite allows easy, efficient and high-throughput measurements on a large number of crystals. The fast continuous diffraction-based two-dimensional grid scan method allows initial location of microcrystals. The CY+ GUI utility enables efficient assessment of a grid scan's analysis output and subsequent collection of multiple wedges of data (so-called minisets) from automatically selected positions in a serial and automated way. The automated data processing (adp) routines adapted to the SSX data collection mode provide near real time analysis for data in both CBF and HDF5 formats. The automatic data merging (adm) is the latest extension of the DA+ data analysis software routines. It utilizes the sxdm (SSX data merging) package, which provides automatic online scaling and merging of minisets and allows identification of a minisets subset resulting in the best quality of the final merged data. The results of both adp and adm are sent to the MX MongoDB database and displayed in the web-based tracker, which provides the user with on-the-fly feedback about the experiment.
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Affiliation(s)
- Shibom Basu
- Swiss Light Source, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Jakub W. Kaminski
- Swiss Light Source, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Ezequiel Panepucci
- Swiss Light Source, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Chia-Ying Huang
- Swiss Light Source, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | | | - Meitian Wang
- Swiss Light Source, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
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44
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A Critical Analysis of Molecular Mechanisms Underlying Membrane Cholesterol Sensitivity of GPCRs. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1115:21-52. [PMID: 30649754 DOI: 10.1007/978-3-030-04278-3_2] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
G protein-coupled receptors (GPCRs) are the largest and a diverse family of proteins involved in signal transduction across biological membranes. GPCRs mediate a wide range of physiological processes and have emerged as major targets for the development of novel drug candidates in all clinical areas. Since GPCRs are integral membrane proteins, regulation of their organization, dynamics, and function by membrane lipids, in particular membrane cholesterol, has emerged as an exciting area of research. Cholesterol sensitivity of GPCRs could be due to direct interaction of cholesterol with the receptor (specific effect). Alternately, GPCR function could be influenced by the effect of cholesterol on membrane physical properties (general effect). In this review, we critically analyze the specific and general mechanisms of the modulation of GPCR function by membrane cholesterol, taking examples from representative GPCRs. While evidence for both the proposed mechanisms exists, there appears to be no clear-cut distinction between these two mechanisms, and a combination of these mechanisms cannot be ruled out in many cases. We conclude that classifying the mechanism underlying cholesterol sensitivity of GPCR function merely into these two mutually exclusive classes could be somewhat arbitrary. A more holistic approach could be suitable for analyzing GPCR-cholesterol interaction.
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45
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Three-dimensional descriptors for aminergic GPCRs: dependence on docking conformation and crystal structure. Mol Divers 2018; 23:603-613. [PMID: 30484023 PMCID: PMC6682580 DOI: 10.1007/s11030-018-9894-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 11/12/2018] [Indexed: 01/01/2023]
Abstract
Three-dimensional descriptors are often used to search for new biologically active compounds, in both ligand- and structure-based approaches, capturing the spatial orientation of molecules. They frequently constitute an input for machine learning-based predictions of compound activity or quantitative structure-activity relationship modeling; however, the distribution of their values and the accuracy of depicting compound orientations might have an impact on the power of the obtained predictive models. In this study, we analyzed the distribution of three-dimensional descriptors calculated for docking poses of active and inactive compounds for all aminergic G protein-coupled receptors with available crystal structures, focusing on the variation in conformations for different receptors and crystals. We demonstrated that the consistency in compound orientation in the binding site is rather not correlated with the affinity itself, but is more influenced by other factors, such as the number of rotatable bonds and crystal structure used for docking studies. The visualizations of the descriptors distributions were prepared and made available online at http://chem.gmum.net/vischem_stability , which enables the investigation of chemical structures referring to particular data points depicted in the figures. Moreover, the performed analysis can assist in choosing crystal structure for docking studies, helping in selection of conditions providing the best discrimination between active and inactive compounds in machine learning-based experiments.
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46
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Vass M, Podlewska S, de Esch IJP, Bojarski AJ, Leurs R, Kooistra AJ, de Graaf C. Aminergic GPCR-Ligand Interactions: A Chemical and Structural Map of Receptor Mutation Data. J Med Chem 2018; 62:3784-3839. [PMID: 30351004 DOI: 10.1021/acs.jmedchem.8b00836] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The aminergic family of G protein-coupled receptors (GPCRs) plays an important role in various diseases and represents a major drug discovery target class. Structure determination of all major aminergic subfamilies has enabled structure-based ligand design for these receptors. Site-directed mutagenesis data provides an invaluable complementary source of information for elucidating the structural determinants of binding of different ligand chemotypes. The current study provides a comparative analysis of 6692 mutation data points on 34 aminergic GPCR subtypes, covering the chemical space of 540 unique ligands from mutagenesis experiments and information from experimentally determined structures of 52 distinct aminergic receptor-ligand complexes. The integrated analysis enables detailed investigation of structural receptor-ligand interactions and assessment of the transferability of combined binding mode and mutation data across ligand chemotypes and receptor subtypes. An overview is provided of the possibilities and limitations of using mutation data to guide the design of novel aminergic receptor ligands.
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Affiliation(s)
- Márton Vass
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS) , VU University Amsterdam , 1081HZ Amsterdam , The Netherlands
| | - Sabina Podlewska
- Department of Medicinal Chemistry, Institute of Pharmacology , Polish Academy of Sciences , Smętna 12 , PL31-343 Kraków , Poland
| | - Iwan J P de Esch
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS) , VU University Amsterdam , 1081HZ Amsterdam , The Netherlands
| | - Andrzej J Bojarski
- Department of Medicinal Chemistry, Institute of Pharmacology , Polish Academy of Sciences , Smętna 12 , PL31-343 Kraków , Poland
| | - Rob Leurs
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS) , VU University Amsterdam , 1081HZ Amsterdam , The Netherlands
| | - Albert J Kooistra
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS) , VU University Amsterdam , 1081HZ Amsterdam , The Netherlands.,Department of Drug Design and Pharmacology , University of Copenhagen , Universitetsparken 2 , 2100 Copenhagen , Denmark
| | - Chris de Graaf
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS) , VU University Amsterdam , 1081HZ Amsterdam , The Netherlands.,Sosei Heptares , Steinmetz Building, Granta Park, Great Abington , Cambridge CB21 6DG , U.K
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47
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Martinez Molledo M, Quistgaard EM, Löw C. Tripeptide binding in a proton-dependent oligopeptide transporter. FEBS Lett 2018; 592:3239-3247. [PMID: 30194725 PMCID: PMC6221056 DOI: 10.1002/1873-3468.13246] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 08/29/2018] [Accepted: 09/05/2018] [Indexed: 01/30/2023]
Abstract
Proton-dependent oligopeptide transporters (POTs) are important for the uptake of di-/tripeptides in many organisms and for drug transport in humans. The binding mode of dipeptides has been well described. However, it is still debated how tripeptides are recognized. Here, we show that tripeptides of the sequence Phe-Ala-Xxx bind with similar affinities as dipeptides to the POT transporter from Streptococcus thermophilus (PepTS t ). We furthermore determined a 2.3-Å structure of PepTS t in complex with Phe-Ala-Gln. The phenylalanine and alanine residues of the peptide adopt the same positions as previously observed for the Phe-Ala dipeptide, while the glutamine side chain extends into a hitherto uncharacterized pocket. This pocket is adaptable in size and can likely accommodate a wide variety of peptide side chains.
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Affiliation(s)
- Maria Martinez Molledo
- Centre for Structural Systems Biology (CSSB), DESY and European Molecular Biology Laboratory Hamburg, Hamburg, Germany
| | - Esben M Quistgaard
- Centre for Structural Systems Biology (CSSB), DESY and European Molecular Biology Laboratory Hamburg, Hamburg, Germany.,Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Christian Löw
- Centre for Structural Systems Biology (CSSB), DESY and European Molecular Biology Laboratory Hamburg, Hamburg, Germany.,Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
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48
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Huang CY, Olieric V, Howe N, Warshamanage R, Weinert T, Panepucci E, Vogeley L, Basu S, Diederichs K, Caffrey M, Wang M. In situ serial crystallography for rapid de novo membrane protein structure determination. Commun Biol 2018; 1:124. [PMID: 30272004 PMCID: PMC6123769 DOI: 10.1038/s42003-018-0123-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 07/19/2018] [Indexed: 11/30/2022] Open
Abstract
De novo membrane protein structure determination is often limited by the availability of large crystals and the difficulties in obtaining accurate diffraction data for experimental phasing. Here we present a method that combines in situ serial crystallography with de novo phasing for fast, efficient membrane protein structure determination. The method enables systematic diffraction screening and rapid data collection from hundreds of microcrystals in in meso crystallization wells without the need for direct crystal harvesting. The requisite data quality for experimental phasing is achieved by accumulating diffraction signals from isomorphous crystals identified post-data collection. The method works in all experimental phasing scenarios and is particularly attractive with fragile, weakly diffracting microcrystals. The automated serial data collection approach can be readily adopted at most microfocus macromolecular crystallography beamlines.
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Affiliation(s)
- Chia-Ying Huang
- Swiss Light Source, Paul Scherrer Institute, CH-5232, Villigen, Switzerland
| | - Vincent Olieric
- Swiss Light Source, Paul Scherrer Institute, CH-5232, Villigen, Switzerland
| | - Nicole Howe
- Membrane Structural and Functional Biology (MS&FB) Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, D02 R590, Ireland
| | | | - Tobias Weinert
- Swiss Light Source, Paul Scherrer Institute, CH-5232, Villigen, Switzerland
| | - Ezequiel Panepucci
- Swiss Light Source, Paul Scherrer Institute, CH-5232, Villigen, Switzerland
| | - Lutz Vogeley
- Membrane Structural and Functional Biology (MS&FB) Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, D02 R590, Ireland
| | - Shibom Basu
- Swiss Light Source, Paul Scherrer Institute, CH-5232, Villigen, Switzerland
| | - Kay Diederichs
- Fachbereich Biologie, Universität Konstanz, M647, D-78457, Konstanz, Germany
| | - Martin Caffrey
- Membrane Structural and Functional Biology (MS&FB) Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, D02 R590, Ireland.
| | - Meitian Wang
- Swiss Light Source, Paul Scherrer Institute, CH-5232, Villigen, Switzerland.
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49
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Birch J, Axford D, Foadi J, Meyer A, Eckhardt A, Thielmann Y, Moraes I. The fine art of integral membrane protein crystallisation. Methods 2018; 147:150-162. [PMID: 29778646 DOI: 10.1016/j.ymeth.2018.05.014] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 05/13/2018] [Accepted: 05/15/2018] [Indexed: 11/29/2022] Open
Abstract
Integral membrane proteins are among the most fascinating and important biomolecules as they play a vital role in many biological functions. Knowledge of their atomic structures is fundamental to the understanding of their biochemical function and key in many drug discovery programs. However, over the years, structure determination of integral membrane proteins has proven to be far from trivial, hence they are underrepresented in the protein data bank. Low expression levels, insolubility and instability are just a few of the many hurdles one faces when studying these proteins. X-ray crystallography has been the most used method to determine atomic structures of membrane proteins. However, the production of high quality membrane protein crystals is always very challenging, often seen more as art than a rational experiment. Here we review valuable approaches, methods and techniques to successful membrane protein crystallisation.
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Affiliation(s)
- James Birch
- Membrane Protein Laboratory, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Danny Axford
- Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE, UK
| | - James Foadi
- Department of Mathematical Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Arne Meyer
- XtalConcepts GmbH, Schnackenburgallee 13, 22525 Hamburg, Germany
| | - Annette Eckhardt
- XtalConcepts GmbH, Schnackenburgallee 13, 22525 Hamburg, Germany
| | - Yvonne Thielmann
- Max Planck Institute of Biophysics, Molecular Membrane Biology, Max-von-Laue-Strasse 3, 60438 Frankfurt, Germany
| | - Isabel Moraes
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK; Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE, UK; National Physical Laboratory, Hampton Road, Teddington TW11 0LW, UK.
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50
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Yamashita K, Hirata K, Yamamoto M. KAMO: towards automated data processing for microcrystals. Acta Crystallogr D Struct Biol 2018; 74:441-449. [PMID: 29717715 PMCID: PMC5930351 DOI: 10.1107/s2059798318004576] [Citation(s) in RCA: 152] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Accepted: 03/19/2018] [Indexed: 01/27/2023] Open
Abstract
In protein microcrystallography, radiation damage often hampers complete and high-resolution data collection from a single crystal, even under cryogenic conditions. One promising solution is to collect small wedges of data (5-10°) separately from multiple crystals. The data from these crystals can then be merged into a complete reflection-intensity set. However, data processing of multiple small-wedge data sets is challenging. Here, a new open-source data-processing pipeline, KAMO, which utilizes existing programs, including the XDS and CCP4 packages, has been developed to automate whole data-processing tasks in the case of multiple small-wedge data sets. Firstly, KAMO processes individual data sets and collates those indexed with equivalent unit-cell parameters. The space group is then chosen and any indexing ambiguity is resolved. Finally, clustering is performed, followed by merging with outlier rejections, and a report is subsequently created. Using synthetic and several real-world data sets collected from hundreds of crystals, it was demonstrated that merged structure-factor amplitudes can be obtained in a largely automated manner using KAMO, which greatly facilitated the structure analyses of challenging targets that only produced microcrystals.
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