1
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He J, Dmochowski IJ. Local Xenon-Protein Interaction Produces Global Conformational Change and Allosteric Inhibition in Lysozyme. Biochemistry 2023; 62:1659-1669. [PMID: 37192381 PMCID: PMC10821772 DOI: 10.1021/acs.biochem.3c00046] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Noble gases have well-established biological effects, yet their molecular mechanisms remain poorly understood. Here, we investigated, both experimentally and computationally, the molecular modes of xenon (Xe) action in bacteriophage T4 lysozyme (T4L). By combining indirect gassing methods with a colorimetric lysozyme activity assay, a reversible, Xe-specific (20 ± 3)% inhibition effect was observed. Accelerated molecular dynamic simulations revealed that Xe exerts allosteric inhibition on the protein by expanding a C-terminal hydrophobic cavity. Xe-induced cavity expansion results in global conformational changes, with long-range transduction distorting the active site where peptidoglycan binds. Interestingly, the peptide substrate binding site that enables lysozyme specificity does not change conformation. Two T4L mutants designed to reshape the C-terminal Xe cavity established a correlation between cavity expansion and enzyme inhibition. This work also highlights the use of Xe flooding simulations to identify new cryptic binding pockets. These results enrich our understanding of Xe-protein interactions at the molecular level and inspire further biochemical investigations with noble gases.
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Affiliation(s)
- Jiayi He
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| | - Ivan J Dmochowski
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
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2
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Ledwitch KV, Künze G, McKinney JR, Okwei E, Larochelle K, Pankewitz L, Ganguly S, Darling HL, Coin I, Meiler J. Sparse pseudocontact shift NMR data obtained from a non-canonical amino acid-linked lanthanide tag improves integral membrane protein structure prediction. JOURNAL OF BIOMOLECULAR NMR 2023; 77:69-82. [PMID: 37016190 PMCID: PMC10443207 DOI: 10.1007/s10858-023-00412-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 03/20/2023] [Indexed: 06/19/2023]
Abstract
A single experimental method alone often fails to provide the resolution, accuracy, and coverage needed to model integral membrane proteins (IMPs). Integrating computation with experimental data is a powerful approach to supplement missing structural information with atomic detail. We combine RosettaNMR with experimentally-derived paramagnetic NMR restraints to guide membrane protein structure prediction. We demonstrate this approach using the disulfide bond formation protein B (DsbB), an α-helical IMP. Here, we attached a cyclen-based paramagnetic lanthanide tag to an engineered non-canonical amino acid (ncAA) using a copper-catalyzed azide-alkyne cycloaddition (CuAAC) click chemistry reaction. Using this tagging strategy, we collected 203 backbone HN pseudocontact shifts (PCSs) for three different labeling sites and used these as input to guide de novo membrane protein structure prediction protocols in Rosetta. We find that this sparse PCS dataset combined with 44 long-range NOEs as restraints in our calculations improves structure prediction of DsbB by enhancements in model accuracy, sampling, and scoring. The inclusion of this PCS dataset improved the Cα-RMSD transmembrane segment values of the best-scoring and best-RMSD models from 9.57 Å and 3.06 Å (no NMR data) to 5.73 Å and 2.18 Å, respectively.
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Affiliation(s)
- Kaitlyn V Ledwitch
- Center for Structural Biology, Vanderbilt University, Nashville, TN, 37240, USA.
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA.
- Department of Chemistry, Center for Structural Biology, MRBIII 5154E, Vanderbilt University, Nashville, TN, 37212, USA.
| | - Georg Künze
- Institute of Drug Discovery, Faculty of Medicine, University of Leipzig, 04103, Leipzig, Germany
| | - Jacob R McKinney
- Center for Structural Biology, Vanderbilt University, Nashville, TN, 37240, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
| | - Elleansar Okwei
- Center for Structural Biology, Vanderbilt University, Nashville, TN, 37240, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
| | - Katherine Larochelle
- Center for Structural Biology, Vanderbilt University, Nashville, TN, 37240, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
| | - Lisa Pankewitz
- Center for Structural Biology, Vanderbilt University, Nashville, TN, 37240, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
| | - Soumya Ganguly
- Center for Structural Biology, Vanderbilt University, Nashville, TN, 37240, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
| | - Heather L Darling
- Center for Structural Biology, Vanderbilt University, Nashville, TN, 37240, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
| | - Irene Coin
- Institute of Biochemistry, Faculty of Life Science, University of Leipzig, 04103, Leipzig, Germany
| | - Jens Meiler
- Center for Structural Biology, Vanderbilt University, Nashville, TN, 37240, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
- Institute of Drug Discovery, Faculty of Medicine, University of Leipzig, 04103, Leipzig, Germany
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3
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Parigi G, Ravera E, Piccioli M, Luchinat C. Paramagnetic NMR restraints for the characterization of protein structural rearrangements. Curr Opin Struct Biol 2023; 80:102595. [PMID: 37075534 DOI: 10.1016/j.sbi.2023.102595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 03/15/2023] [Accepted: 03/17/2023] [Indexed: 04/21/2023]
Abstract
Mobility is a common feature of biomacromolecules, often fundamental for their function. Thus, in many cases, biomacromolecules cannot be described by a single conformation, but rather by a conformational ensemble. NMR paramagnetic data demonstrated quite informative to monitor this conformational variability, especially when used in conjunction with data from different sources. Due to their long-range nature, paramagnetic data can, for instance, i) clearly demonstrate the occurrence of conformational rearrangements, ii) reveal the presence of minor conformational states, sampled only for a short time, iii) indicate the most representative conformations within the conformational ensemble sampled by the molecule, iv) provide an upper limit to the weight of each conformation.
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Affiliation(s)
- Giacomo Parigi
- Magnetic Resonance Center (CERM), University of Florence, Via Sacconi 6, Sesto Fiorentino, 50019, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, Sesto Fiorentino, 50019, Italy; Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Via Sacconi 6, Sesto Fiorentino, 50019, Italy.
| | - Enrico Ravera
- Magnetic Resonance Center (CERM), University of Florence, Via Sacconi 6, Sesto Fiorentino, 50019, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, Sesto Fiorentino, 50019, Italy; Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Via Sacconi 6, Sesto Fiorentino, 50019, Italy
| | - Mario Piccioli
- Magnetic Resonance Center (CERM), University of Florence, Via Sacconi 6, Sesto Fiorentino, 50019, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, Sesto Fiorentino, 50019, Italy; Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Via Sacconi 6, Sesto Fiorentino, 50019, Italy.
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, Via Sacconi 6, Sesto Fiorentino, 50019, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, Sesto Fiorentino, 50019, Italy; Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Via Sacconi 6, Sesto Fiorentino, 50019, Italy.
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4
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Hou XN, Tochio H. Characterizing conformational ensembles of multi-domain proteins using anisotropic paramagnetic NMR restraints. Biophys Rev 2022; 14:55-66. [PMID: 35340613 PMCID: PMC8921464 DOI: 10.1007/s12551-021-00916-4] [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: 09/10/2021] [Accepted: 11/16/2021] [Indexed: 01/13/2023] Open
Abstract
It has been over two decades since paramagnetic NMR started to form part of the essential techniques for structural analysis of proteins under physiological conditions. Paramagnetic NMR has significantly expanded our understanding of the inherent flexibility of proteins, in particular, those that are formed by combinations of two or more domains. Here, we present a brief overview of techniques to characterize conformational ensembles of such multi-domain proteins using paramagnetic NMR restraints produced through anisotropic metals, with a focus on the basics of anisotropic paramagnetic effects, the general procedures of conformational ensemble reconstruction, and some representative reweighting approaches.
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Affiliation(s)
- Xue-Ni Hou
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Hidehito Tochio
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502 Japan
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5
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Müntener T, Joss D, Häussinger D, Hiller S. Pseudocontact Shifts in Biomolecular NMR Spectroscopy. Chem Rev 2022; 122:9422-9467. [PMID: 35005884 DOI: 10.1021/acs.chemrev.1c00796] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Paramagnetic centers in biomolecules, such as specific metal ions that are bound to a protein, affect the nuclei in their surrounding in various ways. One of these effects is the pseudocontact shift (PCS), which leads to strong chemical shift perturbations of nuclear spins, with a remarkably long range of 50 Å and beyond. The PCS in solution NMR is an effect originating from the anisotropic part of the dipole-dipole interaction between the magnetic momentum of unpaired electrons and nuclear spins. The PCS contains spatial information that can be exploited in multiple ways to characterize structure, function, and dynamics of biomacromolecules. It can be used to refine structures, magnify effects of dynamics, help resonance assignments, allows for an intermolecular positioning system, and gives structural information in sensitivity-limited situations where all other methods fail. Here, we review applications of the PCS in biomolecular solution NMR spectroscopy, starting from early works on natural metalloproteins, following the development of non-natural tags to chelate and attach lanthanoid ions to any biomolecular target to advanced applications on large biomolecular complexes and inside living cells. We thus hope to not only highlight past applications but also shed light on the tremendous potential the PCS has in structural biology.
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Affiliation(s)
- Thomas Müntener
- Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Daniel Joss
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland
| | - Daniel Häussinger
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland
| | - Sebastian Hiller
- Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
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6
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Du XZ, Hua XF, Zhang ZY. Choice of force fields and water models for sampling solution conformations of bacteriophage T4 lysozyme. CHINESE J CHEM PHYS 2021. [DOI: 10.1063/1674-0068/cjcp2010184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Xin-zheng Du
- MOE Key Laboratory for Membraneless & Cellular Dynamics, National Science Center for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
| | - Xin-fan Hua
- MOE Key Laboratory for Membraneless & Cellular Dynamics, National Science Center for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
| | - Zhi-yong Zhang
- MOE Key Laboratory for Membraneless & Cellular Dynamics, National Science Center for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
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7
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Miao Q, Zurlo E, de Bruin D, Wondergem JAJ, Timmer M, Blok A, Heinrich D, Overhand M, Huber M, Ubbink M. A Two-Armed Probe for In-Cell DEER Measurements on Proteins*. Chemistry 2020; 26:17128-17133. [PMID: 33200852 PMCID: PMC7839491 DOI: 10.1002/chem.202002743] [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: 06/06/2020] [Revised: 08/27/2020] [Indexed: 12/21/2022]
Abstract
The application of double electron‐electron resonance (DEER) with site‐directed spin labeling (SDSL) to measure distances in proteins and protein complexes in living cells puts rigorous restraints on the spin‐label. The linkage and paramagnetic centers need to resist the reducing conditions of the cell. Rigid attachment of the probe to the protein improves precision of the measured distances. Here, three two‐armed GdIII complexes, GdIII‐CLaNP13a/b/c were synthesized. Rather than the disulfide linkage of most other CLaNP molecules, a thioether linkage was used to avoid reductive dissociation of the linker. The doubly GdIII labeled N55C/V57C/K147C/T151C variants of T4Lysozyme were measured by 95 GHz DEER. The constructs were measured in vitro, in cell lysate and in Dictyostelium discoideum cells. Measured distances were 4.5 nm, consistent with results from paramagnetic NMR. A narrow distance distribution and typical modulation depth, also in cell, indicate complete and durable labeling and probe rigidity due to the dual attachment sites.
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Affiliation(s)
- Qing Miao
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2333, CC, Leiden, The Netherlands
| | - Enrico Zurlo
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, PO box 9504, 2300, RA, Leiden, The Netherlands
| | - Donny de Bruin
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, PO box 9504, 2300, RA, Leiden, The Netherlands
| | - Joeri A J Wondergem
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, PO box 9504, 2300, RA, Leiden, The Netherlands
| | - Monika Timmer
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2333, CC, Leiden, The Netherlands
| | - Anneloes Blok
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2333, CC, Leiden, The Netherlands
| | - Doris Heinrich
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, PO box 9504, 2300, RA, Leiden, The Netherlands.,Fraunhofer Institute for Silicate Research ISC, 97082, Würzburg, Germany
| | - Mark Overhand
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2333, CC, Leiden, The Netherlands
| | - Martina Huber
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, PO box 9504, 2300, RA, Leiden, The Netherlands
| | - Marcellus Ubbink
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2333, CC, Leiden, The Netherlands
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8
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Denis M, Softley C, Giuntini S, Gentili M, Ravera E, Parigi G, Fragai M, Popowicz G, Sattler M, Luchinat C, Cerofolini L, Nativi C. The Photocatalyzed Thiol-ene reaction: A New Tag to Yield Fast, Selective and reversible Paramagnetic Tagging of Proteins. Chemphyschem 2020; 21:863-869. [PMID: 32092218 PMCID: PMC7384118 DOI: 10.1002/cphc.202000071] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 02/21/2020] [Indexed: 11/18/2022]
Abstract
Paramagnetic restraints have been used in biomolecular NMR for the last three decades to elucidate and refine biomolecular structures, but also to characterize protein-ligand interactions. A common technique to generate such restraints in proteins, which do not naturally contain a (paramagnetic) metal, consists in the attachment to the protein of a lanthanide-binding-tag (LBT). In order to design such LBTs, it is important to consider the efficiency and stability of the conjugation, the geometry of the complex (conformational exchanges and coordination) and the chemical inertness of the ligand. Here we describe a photo-catalyzed thiol-ene reaction for the cysteine-selective paramagnetic tagging of proteins. As a model, we designed an LBT with a vinyl-pyridine moiety which was used to attach our tag to the protein GB1 in fast and irreversible fashion. Our tag T1 yields magnetic susceptibility tensors of significant size with different lanthanides and has been characterized using NMR and relaxometry measurements.
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Affiliation(s)
- Maxime Denis
- Giotto Biotech, S.R.LVia Madonna del piano 650019Sesto Fiorentino (FI)Italy
- Department of Chemistry “Ugo Schiff”University of FlorenceVia della Lastruccia 350019Sesto Fiorentino (FI), Italy
| | - Charlotte Softley
- Biomolecular NMR, Department ChemieTechnical University of MunichLichtenbergstrasse 485747GarchingGermany
- Institute of Structural BiologyHelmholtz Center MunichNeuherbergGermany
| | - Stefano Giuntini
- Department of Chemistry “Ugo Schiff”University of FlorenceVia della Lastruccia 350019Sesto Fiorentino (FI), Italy
- Magnetic Resonance Center (CERM)University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (C.I.R.M.M.P)Via L. Sacconi 650019Sesto FIorentino (FI)Italy
| | - Matteo Gentili
- Giotto Biotech, S.R.LVia Madonna del piano 650019Sesto Fiorentino (FI)Italy
| | - Enrico Ravera
- Magnetic Resonance Center (CERM)University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (C.I.R.M.M.P)Via L. Sacconi 650019Sesto FIorentino (FI)Italy
| | - Giacomo Parigi
- Department of Chemistry “Ugo Schiff”University of FlorenceVia della Lastruccia 350019Sesto Fiorentino (FI), Italy
- Magnetic Resonance Center (CERM)University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (C.I.R.M.M.P)Via L. Sacconi 650019Sesto FIorentino (FI)Italy
| | - Marco Fragai
- Department of Chemistry “Ugo Schiff”University of FlorenceVia della Lastruccia 350019Sesto Fiorentino (FI), Italy
- Magnetic Resonance Center (CERM)University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (C.I.R.M.M.P)Via L. Sacconi 650019Sesto FIorentino (FI)Italy
| | - Grzegorz Popowicz
- Institute of Structural BiologyHelmholtz Center MunichNeuherbergGermany
| | - Michael Sattler
- Biomolecular NMR, Department ChemieTechnical University of MunichLichtenbergstrasse 485747GarchingGermany
- Institute of Structural BiologyHelmholtz Center MunichNeuherbergGermany
| | - Claudio Luchinat
- Department of Chemistry “Ugo Schiff”University of FlorenceVia della Lastruccia 350019Sesto Fiorentino (FI), Italy
- Magnetic Resonance Center (CERM)University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (C.I.R.M.M.P)Via L. Sacconi 650019Sesto FIorentino (FI)Italy
| | - Linda Cerofolini
- Magnetic Resonance Center (CERM)University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (C.I.R.M.M.P)Via L. Sacconi 650019Sesto FIorentino (FI)Italy
| | - Cristina Nativi
- Department of Chemistry “Ugo Schiff”University of FlorenceVia della Lastruccia 350019Sesto Fiorentino (FI), Italy
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9
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Joss D, Häussinger D. Design and applications of lanthanide chelating tags for pseudocontact shift NMR spectroscopy with biomacromolecules. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2019; 114-115:284-312. [PMID: 31779884 DOI: 10.1016/j.pnmrs.2019.08.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 08/21/2019] [Accepted: 08/24/2019] [Indexed: 05/14/2023]
Abstract
In this review, lanthanide chelating tags and their applications to pseudocontact shift NMR spectroscopy as well as analysis of residual dipolar couplings are covered. A complete overview is presented of DOTA-derived and non-DOTA-derived lanthanide chelating tags, critical points in the design of lanthanide chelating tags as appropriate linker moieties, their stability under reductive conditions, e.g., for in-cell applications, the magnitude of the anisotropy transferred from the lanthanide chelating tag to the biomacromolecule under investigation and structural properties, as well as conformational bias of the lanthanide chelating tags are discussed. Furthermore, all DOTA-derived lanthanide chelating tags used for PCS NMR spectroscopy published to date are displayed in tabular form, including their anisotropy parameters, with all employed lanthanide ions, CB-Ln distances and tagging reaction conditions, i.e., the stoichiometry of lanthanide chelating tags, pH, buffer composition, temperature and reaction time. Additionally, applications of lanthanide chelating tags for pseudocontact shifts and residual dipolar couplings that have been reported for proteins, protein-protein and protein-ligand complexes, carbohydrates, carbohydrate-protein complexes, nucleic acids and nucleic acid-protein complexes are presented and critically reviewed. The vast and impressive range of applications of lanthanide chelating tags to structural investigations of biomacromolecules in solution clearly illustrates the significance of this particular field of research. The extension of the repertoire of lanthanide chelating tags from proteins to nucleic acids holds great promise for the determination of valuable structural parameters and further developments in characterizing intermolecular interactions.
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Affiliation(s)
- Daniel Joss
- University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland.
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10
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Nunes R, Vila-Viçosa D, Machuqueiro M, Costa PJ. Biomolecular Simulations of Halogen Bonds with a GROMOS Force Field. J Chem Theory Comput 2018; 14:5383-5392. [PMID: 30215528 DOI: 10.1021/acs.jctc.8b00278] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Halogen bonds (XBs) are non-covalent interactions in which halogens (X), acting as electrophiles, interact with Lewis bases. XBs are able to mediate protein-ligand recognition and therefore play an important role in rational drug design. In this context, the development of molecular modeling tools that can tackle XBs is paramount. XBs are predominantly explained by the existence of a positive region on the electrostatic potential of X named the σ-hole. Typically, with molecular mechanics force fields, this region is modeled using a charged extra point (EP) linked to X along the R-X covalent bond axis. In this work, we developed the first EP-based strategy for GROMOS force fields (specifically GROMOS 54A7) using bacteriophage T4 lysozyme in complex with both iodobenzene and iodopentafluorobenzene as a prototype system. Several EP parametrization schemes were tested by adding a virtual interaction site to ligand topologies retrieved from the Automated Topology Builder (ATB) and Repository. Contrary to previous approaches using other force fields, our analysis is based on the capability of each parametrization scheme to sample XBs during MD simulations. Our results indicate that the implementation of an EP at a distance from iodine corresponding to Rmin provides a good qualitative description of XBs in MD simulations, supporting the compatibility of our approach with the GROMOS 54A7 force field.
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Affiliation(s)
- Rafael Nunes
- Centro de Química e Bioquímica, Departamento de Química e Bioquímica, Faculdade de Ciências , Universidade de Lisboa , Campo Grande, 1749-016 Lisboa , Portugal.,BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências , Universidade de Lisboa , Campo Grande, C8 bdg, 1749-016 Lisboa , Portugal.,Centro de Química Estrutural, Faculdade de Ciências , Universidade de Lisboa , Campo Grande, 1749-016 Lisboa , Portugal
| | - Diogo Vila-Viçosa
- Centro de Química e Bioquímica, Departamento de Química e Bioquímica, Faculdade de Ciências , Universidade de Lisboa , Campo Grande, 1749-016 Lisboa , Portugal.,BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências , Universidade de Lisboa , Campo Grande, C8 bdg, 1749-016 Lisboa , Portugal
| | - Miguel Machuqueiro
- Centro de Química e Bioquímica, Departamento de Química e Bioquímica, Faculdade de Ciências , Universidade de Lisboa , Campo Grande, 1749-016 Lisboa , Portugal.,BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências , Universidade de Lisboa , Campo Grande, C8 bdg, 1749-016 Lisboa , Portugal
| | - Paulo J Costa
- Centro de Química e Bioquímica, Departamento de Química e Bioquímica, Faculdade de Ciências , Universidade de Lisboa , Campo Grande, 1749-016 Lisboa , Portugal.,BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências , Universidade de Lisboa , Campo Grande, C8 bdg, 1749-016 Lisboa , Portugal
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11
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Chen JL, Zhao Y, Gong YJ, Pan BB, Wang X, Su XC. Stable and rigid DTPA-like paramagnetic tags suitable for in vitro and in situ protein NMR analysis. JOURNAL OF BIOMOLECULAR NMR 2018; 70:77-92. [PMID: 29224182 DOI: 10.1007/s10858-017-0160-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 12/05/2017] [Indexed: 06/07/2023]
Abstract
Organic synthesis of a ligand with high binding affinities for paramagnetic lanthanide ions is an effective way of generating paramagnetic effects on proteins. These paramagnetic effects manifested in high-resolution NMR spectroscopy are valuable dynamic and structural restraints of proteins and protein-ligand complexes. A paramagnetic tag generally contains a metal chelating moiety and a reactive group for protein modification. Herein we report two new DTPA-like tags, 4PS-PyDTTA and 4PS-6M-PyDTTA that can be site-specifically attached to a protein with a stable thioether bond. Both protein-tag adducts form stable lanthanide complexes, of which the binding affinities and paramagnetic tensors are tunable with respect to the 6-methyl group in pyridine. Paramagnetic relaxation enhancement (PRE) effects of Gd(III) complex on protein-tag adducts were evaluated in comparison with pseudocontact shift (PCS), and the results indicated that both 4PS-PyDTTA and 4PS-6M-PyDTTA tags are rigid and present high-quality PREs that are crucially important in elucidation of the dynamics and interactions of proteins and protein-ligand complexes. We also show that these two tags are suitable for in-situ protein NMR analysis.
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Affiliation(s)
- Jia-Liang Chen
- State Key Laboratory of Elemento-Organic Chemistry and Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Yu Zhao
- State Key Laboratory of Elemento-Organic Chemistry and Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Yan-Jun Gong
- State Key Laboratory of Elemento-Organic Chemistry and Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Bin-Bin Pan
- State Key Laboratory of Elemento-Organic Chemistry and Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Xiao Wang
- State Key Laboratory of Elemento-Organic Chemistry and Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-Organic Chemistry and Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), College of Chemistry, Nankai University, Tianjin, 300071, China.
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12
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Welegedara AP, Yang Y, Lee MD, Swarbrick JD, Huber T, Graham B, Goldfarb D, Otting G. Double‐Arm Lanthanide Tags Deliver Narrow Gd
3+
–Gd
3+
Distance Distributions in Double Electron–Electron Resonance (DEER) Measurements. Chemistry 2017; 23:11694-11702. [DOI: 10.1002/chem.201702521] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Adarshi P. Welegedara
- Research School of Chemistry Australian National University Canberra ACT 2601 Australia
| | - Yin Yang
- Department of Chemical Physics Weizmann Institute of Science Rehovot 7610001 Israel
| | - Michael D. Lee
- Monash Institute of Pharmaceutical Sciences Monash University Parkville VIC 3052 Australia
| | - James D. Swarbrick
- Monash Institute of Pharmaceutical Sciences Monash University Parkville VIC 3052 Australia
| | - Thomas Huber
- Research School of Chemistry Australian National University Canberra ACT 2601 Australia
| | - Bim Graham
- Monash Institute of Pharmaceutical Sciences Monash University Parkville VIC 3052 Australia
| | - Daniella Goldfarb
- Department of Chemical Physics Weizmann Institute of Science Rehovot 7610001 Israel
| | - Gottfried Otting
- Research School of Chemistry Australian National University Canberra ACT 2601 Australia
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13
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Nitsche C, Otting G. Pseudocontact shifts in biomolecular NMR using paramagnetic metal tags. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2017; 98-99:20-49. [PMID: 28283085 DOI: 10.1016/j.pnmrs.2016.11.001] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/11/2016] [Accepted: 11/12/2016] [Indexed: 05/14/2023]
Affiliation(s)
- Christoph Nitsche
- Australian National University, Research School of Chemistry, Canberra, ACT 2601, Australia.
| | - Gottfried Otting
- Australian National University, Research School of Chemistry, Canberra, ACT 2601, Australia. http://www.rsc.anu.edu.au/~go/index.html
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14
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Ma FH, Wang X, Chen JL, Wen X, Sun H, Su XC. Deciphering the Multisite Interactions of a Protein and Its Ligand at Atomic Resolution by Using Sensitive Paramagnetic Effects. Chemistry 2017; 23:926-934. [DOI: 10.1002/chem.201604393] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Indexed: 11/12/2022]
Affiliation(s)
- Fei-He Ma
- State Key Laboratory of Elemento-Organic Chemistry and Collaborative, Innovation Center of Chemical Science and Engineering (Tianjin); Nankai University; Tianjin 300071 China
| | - Xiao Wang
- State Key Laboratory of Elemento-Organic Chemistry and Collaborative, Innovation Center of Chemical Science and Engineering (Tianjin); Nankai University; Tianjin 300071 China
| | - Jia-Liang Chen
- State Key Laboratory of Elemento-Organic Chemistry and Collaborative, Innovation Center of Chemical Science and Engineering (Tianjin); Nankai University; Tianjin 300071 China
| | - Xin Wen
- State Key Laboratory of Elemento-Organic Chemistry and Collaborative, Innovation Center of Chemical Science and Engineering (Tianjin); Nankai University; Tianjin 300071 China
| | - Han Sun
- Department of Structural Biology; Leibniz-Institut für Molekulare Pharmakologie (FMP); Robert-Roessle-Str. 10 13125 Berlin Germany
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-Organic Chemistry and Collaborative, Innovation Center of Chemical Science and Engineering (Tianjin); Nankai University; Tianjin 300071 China
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15
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Yang F, Wang X, Pan BB, Su XC. Single-armed phenylsulfonated pyridine derivative of DOTA is rigid and stable paramagnetic tag in protein analysis. Chem Commun (Camb) 2016; 52:11535-11538. [DOI: 10.1039/c6cc06114a] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Single-armed DOTA-like phenylsulfonated pyridine derivatives are rigid and stable paramagnetic tags for site-specific labelling of proteins. The respective protein conjugates yield valuable long-range structural restraints for proteins.
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Affiliation(s)
- Feng Yang
- State Key Laboratory of Elemento-Organic Chemistry
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
- Nankai University
- Tianjin 300071
- China
| | - Xiao Wang
- State Key Laboratory of Elemento-Organic Chemistry
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
- Nankai University
- Tianjin 300071
- China
| | - Bin-Bin Pan
- State Key Laboratory of Elemento-Organic Chemistry
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
- Nankai University
- Tianjin 300071
- China
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-Organic Chemistry
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
- Nankai University
- Tianjin 300071
- China
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