1
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Zeindl R, Franzmann AL, Fernández-Quintero ML, Seidler CA, Hoerschinger VJ, Liedl KR, Tollinger M. Structural Basis of the Immunological Cross-Reactivity between Kiwi and Birch Pollen. Foods 2023; 12:3939. [PMID: 37959058 PMCID: PMC10649968 DOI: 10.3390/foods12213939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023] Open
Abstract
Allergies related to kiwi consumption have become a growing health concern, with their prevalence on the rise. Many of these allergic reactions are attributed to cross-reactivity, particularly with the major allergen found in birch pollen. This cross-reactivity is associated with proteins belonging to the pathogenesis-related class 10 (PR-10) protein family. In our study, we determined the three-dimensional structures of the two PR-10 proteins in gold and green kiwi fruits, Act c 8 and Act d 8, using nuclear magnetic resonance (NMR) spectroscopy. The structures of both kiwi proteins closely resemble the major birch pollen allergen, Bet v 1, providing a molecular explanation for the observed immunological cross-reactivity between kiwi and birch pollen. Compared to Act d 11, however, a kiwi allergen that shares the same architecture as PR-10 proteins, structural differences are apparent. Moreover, despite both Act c 8 and Act d 8 containing multiple cysteine residues, no disulfide bridges are present within their structures. Instead, all the cysteines are accessible on the protein's surface and exposed to the surrounding solvent, where they are available for reactions with components of the natural food matrix. This structural characteristic sets Act c 8 and Act d 8 apart from other kiwi proteins with a high cysteine content. Furthermore, we demonstrate that pyrogallol, the most abundant phenolic compound found in kiwi, binds into the internal cavities of these two proteins, albeit with low affinity. Our research offers a foundation for further studies aimed at understanding allergic reactions associated with this fruit and exploring how interactions with the natural food matrix might be employed to enhance food safety.
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Affiliation(s)
- Ricarda Zeindl
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria; (R.Z.); (A.L.F.)
| | - Annika L. Franzmann
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria; (R.Z.); (A.L.F.)
| | - Monica L. Fernández-Quintero
- Institute of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria; (M.L.F.-Q.); (C.A.S.); (K.R.L.)
| | - Clarissa A. Seidler
- Institute of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria; (M.L.F.-Q.); (C.A.S.); (K.R.L.)
| | - Valentin J. Hoerschinger
- Institute of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria; (M.L.F.-Q.); (C.A.S.); (K.R.L.)
| | - Klaus R. Liedl
- Institute of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria; (M.L.F.-Q.); (C.A.S.); (K.R.L.)
| | - Martin Tollinger
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria; (R.Z.); (A.L.F.)
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2
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Chen E, Widjaja V, Kyro G, Allen B, Das P, Prahaladan VM, Bhandari V, Lolis EJ, Batista VS, Lisi GP. Mapping N- to C-terminal allosteric coupling through disruption of a putative CD74 activation site in D-dopachrome tautomerase. J Biol Chem 2023; 299:104729. [PMID: 37080391 PMCID: PMC10208890 DOI: 10.1016/j.jbc.2023.104729] [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: 12/16/2022] [Revised: 04/12/2023] [Accepted: 04/15/2023] [Indexed: 04/22/2023] Open
Abstract
The macrophage migration inhibitory factor (MIF) protein family consists of MIF and D-dopachrome tautomerase (also known as MIF-2). These homologs share 34% sequence identity while maintaining nearly indistinguishable tertiary and quaternary structure, which is likely a major contributor to their overlapping functions, including the binding and activation of the cluster of differentiation 74 (CD74) receptor to mediate inflammation. Previously, we investigated a novel allosteric site, Tyr99, that modulated N-terminal catalytic activity in MIF through a "pathway" of dynamically coupled residues. In a comparative study, we revealed an analogous allosteric pathway in MIF-2 despite its unique primary sequence. Disruptions of the MIF and MIF-2 N termini also diminished CD74 activation at the C terminus, though the receptor activation site is not fully defined in MIF-2. In this study, we use site-directed mutagenesis, NMR spectroscopy, molecular simulations, in vitro and in vivo biochemistry to explore the putative CD74 activation region of MIF-2 based on homology to MIF. We also confirm its reciprocal structural coupling to the MIF-2 allosteric site and N-terminal enzymatic site. Thus, we provide further insight into the CD74 activation site of MIF-2 and its allosteric coupling for immunoregulation.
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Affiliation(s)
- Emily Chen
- Department of Molecular Biology, Cell Biology, & Biochemistry, Brown University, Providence, Rhode Island, USA
| | - Vinnie Widjaja
- Department of Molecular Biology, Cell Biology, & Biochemistry, Brown University, Providence, Rhode Island, USA
| | - Gregory Kyro
- Department of Chemistry, Yale University, New Haven, Connecticut, USA
| | - Brandon Allen
- Department of Chemistry, Yale University, New Haven, Connecticut, USA
| | - Pragnya Das
- Section of Neonatology, Department of Pediatrics, Cooper University Hospital, Camden, New Jersey, USA
| | - Varsha M Prahaladan
- Section of Neonatology, Department of Pediatrics, Cooper University Hospital, Camden, New Jersey, USA
| | - Vineet Bhandari
- Section of Neonatology, Department of Pediatrics, Cooper University Hospital, Camden, New Jersey, USA
| | - Elias J Lolis
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Victor S Batista
- Department of Chemistry, Yale University, New Haven, Connecticut, USA.
| | - George P Lisi
- Department of Molecular Biology, Cell Biology, & Biochemistry, Brown University, Providence, Rhode Island, USA.
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3
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Wasilewicz A, Kirchweger B, Bojkova D, Abi Saad MJ, Langeder J, Bütikofer M, Adelsberger S, Grienke U, Cinatl
Jr. J, Petermann O, Scapozza L, Orts J, Kirchmair J, Rabenau HF, Rollinger JM. Identification of Natural Products Inhibiting SARS-CoV-2 by Targeting Viral Proteases: A Combined in Silico and in Vitro Approach. JOURNAL OF NATURAL PRODUCTS 2023; 86:264-275. [PMID: 36651644 PMCID: PMC9885530 DOI: 10.1021/acs.jnatprod.2c00843] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Indexed: 05/24/2023]
Abstract
In this study, an integrated in silico-in vitro approach was employed to discover natural products (NPs) active against SARS-CoV-2. The two SARS-CoV-2 viral proteases, i.e., main protease (Mpro) and papain-like protease (PLpro), were selected as targets for the in silico study. Virtual hits were obtained by docking more than 140,000 NPs and NP derivatives available in-house and from commercial sources, and 38 virtual hits were experimentally validated in vitro using two enzyme-based assays. Five inhibited the enzyme activity of SARS-CoV-2 Mpro by more than 60% at a concentration of 20 μM, and four of them with high potency (IC50 < 10 μM). These hit compounds were further evaluated for their antiviral activity against SARS-CoV-2 in Calu-3 cells. The results from the cell-based assay revealed three mulberry Diels-Alder-type adducts (MDAAs) from Morus alba with pronounced anti-SARS-CoV-2 activities. Sanggenons C (12), O (13), and G (15) showed IC50 values of 4.6, 8.0, and 7.6 μM and selectivity index values of 5.1, 3.1 and 6.5, respectively. The docking poses of MDAAs in SARS-CoV-2 Mpro proposed a butterfly-shaped binding conformation, which was supported by the results of saturation transfer difference NMR experiments and competitive 1H relaxation dispersion NMR spectroscopy.
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Affiliation(s)
- Andreas Wasilewicz
- Department
of Pharmaceutical Sciences, University of
Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria
- Vienna
Doctoral School of Pharmaceutical, Nutritional and Sport Sciences, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria
| | - Benjamin Kirchweger
- Department
of Pharmaceutical Sciences, University of
Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria
| | - Denisa Bojkova
- Institute
of Medical Virology, University Hospital
Frankfurt, Paul-Ehrlich-Straße
40, 60596 Frankfurt
am Main, Germany
| | - Marie Jose Abi Saad
- Department
of Pharmaceutical Sciences, University of
Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria
- Vienna
Doctoral School of Pharmaceutical, Nutritional and Sport Sciences, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria
| | - Julia Langeder
- Department
of Pharmaceutical Sciences, University of
Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria
- Vienna
Doctoral School of Pharmaceutical, Nutritional and Sport Sciences, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria
| | - Matthias Bütikofer
- Swiss
Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, 8093 Zurich, Switzerland
| | - Sigrid Adelsberger
- Department
of Pharmaceutical Sciences, University of
Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria
- Vienna
Doctoral School of Pharmaceutical, Nutritional and Sport Sciences, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria
| | - Ulrike Grienke
- Department
of Pharmaceutical Sciences, University of
Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria
| | - Jindrich Cinatl
Jr.
- Institute
of Medical Virology, University Hospital
Frankfurt, Paul-Ehrlich-Straße
40, 60596 Frankfurt
am Main, Germany
| | - Olivier Petermann
- Pharmaceutical
Biochemistry Group, School of Pharmaceutical Sciences, University of Geneva, 1205 Geneva, Switzerland
- Institute
of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1205 Geneva, Switzerland
| | - Leonardo Scapozza
- Pharmaceutical
Biochemistry Group, School of Pharmaceutical Sciences, University of Geneva, 1205 Geneva, Switzerland
- Institute
of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1205 Geneva, Switzerland
| | - Julien Orts
- Department
of Pharmaceutical Sciences, University of
Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria
| | - Johannes Kirchmair
- Department
of Pharmaceutical Sciences, University of
Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria
| | - Holger F. Rabenau
- Institute
of Medical Virology, University Hospital
Frankfurt, Paul-Ehrlich-Straße
40, 60596 Frankfurt
am Main, Germany
| | - Judith M. Rollinger
- Department
of Pharmaceutical Sciences, University of
Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria
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4
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Sánchez HR. Residence Times from Molecular Dynamics Simulations. J Phys Chem B 2022; 126:8804-8812. [PMID: 36269165 DOI: 10.1021/acs.jpcb.2c03756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
In this work, efficient methods are proposed for the calculation, from molecular dynamics trajectories, of residence times (RTs) and related quantities. One of these was designed to obtain RT distributions, from which mean residence times (MRTs), residual time distributions, and mean residual times can be computed. This method does not require the assumptions and approximations made by the most commonly used methods. Its link to the most popular method in the literature is identified. It is shown how the much faster new method can be used as a replacement for the latter and the advantages of doing so. Also, a prescription for estimating the uncertainty in the MRTs obtained though the proposed method is provided. Another even faster method for the calculation of the MRTs, their uncertainties, and the mean residual times is also proposed. It yields exactly the same results as the first one but does not allow to obtain the mentioned distributions. Another very popular method, based on autocorrelation functions, for computing MRTs is analyzed in terms of its assumptions and approximations. An alternative, also based on autocorrelation functions, which is faster and requires fewer assumptions is presented. A prescription for the calculation of the uncertainty of the MRTs obtained with the latter method is also provided. In the literature, there are a few methods to discard short transient escapes. Here, an algorithm is suggested that is much faster than the most used one and allows a more integral treatment of the process. Also, it is more widely applicable because it is a preprocessing step that can be used in conjunction with any of the proposed methods mentioned above. The main disadvantage of these two approaches to discard brief escapes is that the maximum duration allowed for an escape to be considered transient appears as a parameter to be determined for the particular system under study. As an alternative, a parameter-free method of a similar character is also proposed to estimate the mean residence time of particles that reached a constant probability of leaving the region of interest.
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Affiliation(s)
- Hernán R Sánchez
- Instituto de Física de Líquidos y Sistemas Biológicos, UNLP-CONICET, La Plata1900, Argentina
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5
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Führer S, Unterhauser J, Zeindl R, Eidelpes R, Fernández-Quintero ML, Liedl KR, Tollinger M. The Structural Flexibility of PR-10 Food Allergens. Int J Mol Sci 2022; 23:ijms23158252. [PMID: 35897827 PMCID: PMC9330593 DOI: 10.3390/ijms23158252] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 07/22/2022] [Accepted: 07/23/2022] [Indexed: 12/18/2022] Open
Abstract
PR-10 proteins constitute a major cause of food allergic reactions. Birch-pollen-related food allergies are triggered by the immunologic cross-reactivity of IgE antibodies with structurally homologous PR-10 proteins that are present in birch pollen and various food sources. While the three-dimensional structures of PR-10 food allergens have been characterized in detail, only a few experimental studies have addressed the structural flexibility of these proteins. In this study, we analyze the millisecond-timescale structural flexibility of thirteen PR-10 proteins from prevalent plant food sources by NMR relaxation-dispersion spectroscopy, in a comparative manner. We show that all the allergens in this study have inherently flexible protein backbones in solution, yet the extent of the structural flexibility appears to be strikingly protein-specific (but not food-source-specific). Above-average flexibility is present in the two short helices, α1 and α2, which form a V-shaped support for the long C-terminal helix α3, and shape the internal ligand-binding cavity, which is characteristic for PR-10 proteins. An in-depth analysis of the NMR relaxation-dispersion data for the PR-10 allergen from peanut reveals the presence of at least two subglobal conformational transitions on the millisecond timescale, which may be related to the release of bound low-molecular-weight ligands from the internal cavity.
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Affiliation(s)
- Sebastian Führer
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria; (S.F.); (J.U.); (R.Z.); (R.E.)
| | - Jana Unterhauser
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria; (S.F.); (J.U.); (R.Z.); (R.E.)
| | - Ricarda Zeindl
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria; (S.F.); (J.U.); (R.Z.); (R.E.)
| | - Reiner Eidelpes
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria; (S.F.); (J.U.); (R.Z.); (R.E.)
| | - Monica L. Fernández-Quintero
- Department of General, Inorganic and Theoretical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria; (M.L.F.-Q.); (K.R.L.)
| | - Klaus R. Liedl
- Department of General, Inorganic and Theoretical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria; (M.L.F.-Q.); (K.R.L.)
| | - Martin Tollinger
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria; (S.F.); (J.U.); (R.Z.); (R.E.)
- Correspondence: ; Tel.: +43-512-504-57730
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6
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Qi C, Wang Y, Hilty C. Application of Relaxation Dispersion of Hyperpolarized 13 C Spins to Protein-Ligand Binding. Angew Chem Int Ed Engl 2021; 60:24018-24021. [PMID: 34468077 DOI: 10.1002/anie.202109430] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Indexed: 11/11/2022]
Abstract
Nuclear spin relaxation dispersion parameters are proposed as indicators of the binding mode of a ligand to a protein. Hyperpolarization by dissolution dynamic nuclear polarization (D-DNP) provided a 13 C signal enhancement between 3000-6000 for the ligand 4-(trifluoromethyl) benzene-1-carboximidamide binding to trypsin. The measurement of 13 C R2 relaxation dispersion was enabled without isotope enrichment, using a series of single-scan Carr-Purcell-Meiboom-Gill experiments with variable refocusing delays. The magnitude in dispersion for the spins of the ligand is correlated to the position with respect to the salt bridge between protein and the amidine group of the ligand, indicating the ligand binding orientation. Hyperpolarized relaxation dispersion is an alternative to chemical shift or NOE measurements for determining ligand binding modes.
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Affiliation(s)
- Chang Qi
- Chemistry Department, Texas A&M University, 3255 TAMU, College Station, TX, USA
| | - Yunyi Wang
- Chemistry Department, Texas A&M University, 3255 TAMU, College Station, TX, USA
| | - Christian Hilty
- Chemistry Department, Texas A&M University, 3255 TAMU, College Station, TX, USA
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7
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Qi C, Wang Y, Hilty C. Application of Relaxation Dispersion of Hyperpolarized
13
C Spins to Protein–Ligand Binding. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202109430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Chang Qi
- Chemistry Department Texas A&M University 3255 TAMU College Station TX USA
| | - Yunyi Wang
- Chemistry Department Texas A&M University 3255 TAMU College Station TX USA
| | - Christian Hilty
- Chemistry Department Texas A&M University 3255 TAMU College Station TX USA
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8
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Almeida TB, Panova S, Walser R. NMR Reporter Assays for the Quantification of Weak-Affinity Receptor-Ligand Interactions. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2021; 26:1020-1028. [PMID: 33899548 DOI: 10.1177/24725552211009782] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Biophysical methods are widely employed in academia and the pharmaceutical industry to detect and quantify weak molecular interactions. Such methods find broad application in fragment-based drug discovery (FBDD). In an FBDD campaign, a suitable affinity determination method is key to advancing a project beyond the initial screening phase. Protein-observed (PO) nuclear magnetic resonance (NMR) finds widespread use due to its ability to sensitively detect very weak interactions at residue-level resolution. When there are issues precluding the use of PO-NMR, ligand-observed (LO) NMR reporter assays can be a useful alternative. Such assays can measure affinities in a similar range to PO-NMR while offering some distinct advantages, especially with regard to protein consumption and compound throughput. In this paper, we take a closer look at setting up such assays for routine use, with the aim of getting high-quality, accurate data and good throughput. We assess some of the key characteristics of these assays in the mathematical framework established for fluorescence polarization assays with which the readers may be more familiar. We also provide guidance on setting up such assays and compare their performance with other affinity determination methods that are commonly used in drug discovery.
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Affiliation(s)
| | | | - Reto Walser
- Molecular Sciences, Astex Pharmaceuticals, Cambridge, UK
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9
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Eidelpes R, Hofer F, Röck M, Führer S, Kamenik AS, Liedl KR, Tollinger M. Structure and Zeatin Binding of the Peach Allergen Pru p 1. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:8120-8129. [PMID: 34260238 PMCID: PMC8323099 DOI: 10.1021/acs.jafc.1c01876] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 06/18/2021] [Accepted: 07/02/2021] [Indexed: 05/29/2023]
Abstract
Peach (Prunus persica) is among the fruits most frequently reported to cause food allergies. Allergic reactions commonly result from previous sensitization to the birch pollen allergen Bet v 1, followed by immunological cross-reactivity of IgE antibodies to structurally related proteins in peach. In this study, we present the three-dimensional NMR solution structure of the cross-reactive peach allergen Pru p 1 (isoform Pru p 1.0101). This 17.5 kDa protein adopts the canonical Bet v 1 fold, composed of a seven-stranded β-sheet and three α-helices enclosing an internal cavity. In Pru p 1, the inner surface of the cavity contains an array of hydroxyl-bearing amino acids surrounded by a hydrophobic patch, constituting a docking site for amphiphilic molecules. NMR-guided docking of the cytokinin molecule zeatin to the internal cavity of Pru p 1 provides a structure-based rationale for the effect that zeatin binding has on the protein's RNase activity.
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Affiliation(s)
- Reiner Eidelpes
- Institute
of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Florian Hofer
- Institute
of General, Inorganic and Theoretical Chemistry, Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Manuel Röck
- Institute
of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Sebastian Führer
- Institute
of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Anna Sophia Kamenik
- Institute
of General, Inorganic and Theoretical Chemistry, Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Klaus R. Liedl
- Institute
of General, Inorganic and Theoretical Chemistry, Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Martin Tollinger
- Institute
of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
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10
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Lokesh N, Hioe J, Gramüller J, Gschwind RM. Relaxation Dispersion NMR to Reveal Fast Dynamics in Brønsted Acid Catalysis: Influence of Sterics and H-Bond Strength on Conformations and Substrate Hopping. J Am Chem Soc 2019; 141:16398-16407. [PMID: 31545037 PMCID: PMC6863621 DOI: 10.1021/jacs.9b07841] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Indexed: 12/25/2022]
Abstract
NMR provides both structural and dynamic information, which is key to connecting intermediates and to understanding reaction pathways. However, fast exchanging catalytic intermediates are often inaccessible by conventional NMR due its limited time resolution. Here, we show the combined application of the 1H off-resonance R1ρ NMR method and low temperature (185-175 K) to resolve intermediates exchanging on a μs time scale (ns at room temperature). The potential of the approach is demonstrated on chiral phosphoric acid (CPA) catalysts in their complexes with imines. The otherwise inaccessible exchange kinetics of the E-I ⇌ E-II imine conformations and thermodynamic E-I:E-II imine ratios inside the catalyst pocket are experimentally determined and corroborated by calculations. The E-I ⇌ E-II exchange rate constants (kex185 K) for different catalyst-substrate binary complexes varied between 2500 and 19 000 s-1 (τex = 500-50 μs). Theoretical analysis of these exchange rate constants revealed the involvement of an intermediary tilted conformation E-III, which structurally resembles the hydride transfer transition state. The main E-I and E-II exchange pathway is a hydrogen bond strength dependent tilting-switching-tilting mechanism via a bifurcated hydrogen bond as a transition state. The reduction in the sterics of the catalyst showed an accelerated switching process by at least an order of magnitude and enabled an additional rotational pathway. Hence, the exchange process is mainly a function of the intrinsic properties of the 3,3'-substituents of the catalyst. Overall, we believe that the present study opens a new dimension in catalysis via experimental access to structures, populations, and kinetics of catalyst-substrate complexes on the μs time scale by the 1H off-resonance R1ρ method.
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Affiliation(s)
- N. Lokesh
- Institute of Organic Chemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Johnny Hioe
- Institute of Organic Chemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Johannes Gramüller
- Institute of Organic Chemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Ruth M. Gschwind
- Institute of Organic Chemistry, University of Regensburg, D-93053 Regensburg, Germany
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11
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Calabrese DR, Connelly CM, Schneekloth JS. Ligand-observed NMR techniques to probe RNA-small molecule interactions. Methods Enzymol 2019; 623:131-149. [PMID: 31239044 DOI: 10.1016/bs.mie.2019.05.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A growing understanding of the structure and function of RNA has revealed it as a key regulator of gene expression and disease. A multitude of noncoding functions apart from the central roles of RNA in coding for and facilitating protein biogenesis has stimulated research into RNA as a pharmacological target. Despite many exciting advances, RNA remains an understudied target for small molecules, and techniques to investigate RNA-binding molecules are still emerging. A key stumbling block in this area has been validation of RNA-small molecule interactions. Our laboratory has recently used multiple ligand-observed NMR techniques in this regard, including CPMG and WaterLOGSY. This work describes methods to use these techniques in the context of studying RNA-ligand interactions.
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Affiliation(s)
- David R Calabrese
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD, United States
| | - Colleen M Connelly
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD, United States
| | - John S Schneekloth
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD, United States.
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12
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Rangadurai A, Szymaski ES, Kimsey IJ, Shi H, Al-Hashimi HM. Characterizing micro-to-millisecond chemical exchange in nucleic acids using off-resonance R 1ρ relaxation dispersion. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2019; 112-113:55-102. [PMID: 31481159 PMCID: PMC6727989 DOI: 10.1016/j.pnmrs.2019.05.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 05/09/2019] [Accepted: 05/10/2019] [Indexed: 05/10/2023]
Abstract
This review describes off-resonance R1ρ relaxation dispersion NMR methods for characterizing microsecond-to-millisecond chemical exchange in uniformly 13C/15N labeled nucleic acids in solution. The review opens with a historical account of key developments that formed the basis for modern R1ρ techniques used to study chemical exchange in biomolecules. A vector model is then used to describe the R1ρ relaxation dispersion experiment, and how the exchange contribution to relaxation varies with the amplitude and frequency offset of an applied spin-locking field, as well as the population, exchange rate, and differences in chemical shifts of two exchanging species. Mathematical treatment of chemical exchange based on the Bloch-McConnell equations is then presented and used to examine relaxation dispersion profiles for more complex exchange scenarios including three-state exchange. Pulse sequences that employ selective Hartmann-Hahn cross-polarization transfers to excite individual 13C or 15N spins are then described for measuring off-resonance R1ρ(13C) and R1ρ(15N) in uniformly 13C/15N labeled DNA and RNA samples prepared using commercially available 13C/15N labeled nucleotide triphosphates. Approaches for analyzing R1ρ data measured at a single static magnetic field to extract a full set of exchange parameters are then presented that rely on numerical integration of the Bloch-McConnell equations or the use of algebraic expressions. Methods for determining structures of nucleic acid excited states are then reviewed that rely on mutations and chemical modifications to bias conformational equilibria, as well as structure-based approaches to calculate chemical shifts. Applications of the methodology to the study of DNA and RNA conformational dynamics are reviewed and the biological significance of the exchange processes is briefly discussed.
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Affiliation(s)
- Atul Rangadurai
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Eric S Szymaski
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Isaac J Kimsey
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA; Nymirum, 4324 S. Alston Avenue, Durham, NC 27713, USA(1)
| | - Honglue Shi
- Department of Chemistry, Duke University, Durham, NC 27710, USA
| | - Hashim M Al-Hashimi
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA; Department of Chemistry, Duke University, Durham, NC 27710, USA.
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13
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Polshakov VI, Batuev EA, Mantsyzov AB. NMR screening and studies of target–ligand interactions. RUSSIAN CHEMICAL REVIEWS 2019. [DOI: 10.1070/rcr4836] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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14
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Chaubey B, Pal S. Binding Interaction of Organofluorine–Serum Albumin: A Comparative Ligand-Detected 19F NMR Analysis. J Phys Chem B 2018; 122:9409-9418. [DOI: 10.1021/acs.jpcb.8b06583] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Bhawna Chaubey
- Department of Chemistry, Indian Institute of Technology Jodhpur, Jodhpur 342037, India
| | - Samanwita Pal
- Department of Chemistry, Indian Institute of Technology Jodhpur, Jodhpur 342037, India
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15
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Resolving biomolecular motion and interactions by R2 and R1ρ relaxation dispersion NMR. Methods 2018; 148:28-38. [DOI: 10.1016/j.ymeth.2018.04.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 04/18/2018] [Accepted: 04/20/2018] [Indexed: 12/16/2022] Open
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16
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Xu D, Li B, Gao J, Liu Z, Niu X, Nshogoza G, Zhang J, Wu J, Su XC, He W, Ma R, Yang D, Ruan K. Ligand Proton Pseudocontact Shifts Determined from Paramagnetic Relaxation Dispersion in the Limit of NMR Intermediate Exchange. J Phys Chem Lett 2018; 9:3361-3367. [PMID: 29864276 DOI: 10.1021/acs.jpclett.8b01443] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Delineation of protein-ligand interaction modes is key for rational drug discovery. The availability of complex crystal structures is often limited by the aqueous solubility of the compounds, while lead-like compounds with micromolar affinities normally fall into the NMR intermediate exchange regime, in which severe line broadening to beyond the detection of interfacial resonances limits NMR applications. Here, we developed a new method to retrieve low-populated bound-state 1H pseudocontact shifts (PCSs) using paramagnetic relaxation dispersion (RD). We evaluated using a 1H PCS-RD approach in a BRM bromodomain lead-like inhibitor to filter molecular docking poses using multiple intermolecular structural restraints. Considering the universal presence of proton atoms in druglike compounds, our work will have wide application in structure-guided drug discovery even under an extreme condition of NMR intermediate exchange and low aqueous solubility of ligands.
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Affiliation(s)
- Difei Xu
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences , University of Science and Technology of China , Hefei , Anhui 230027 , PR China
| | - Bin Li
- Department of Pharmacology and Pharmaceutical Sciences, School of Medicine, Tsinghua-Peking Joint Center for Life Sciences , Tsinghua University , Beijing , 100084 , PR China
| | - Jia Gao
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences , University of Science and Technology of China , Hefei , Anhui 230027 , PR China
- Center of Medical Physics and Technology, Hefei Institute of Physical Science , Cancer Hospital Chinese Academy of Science , Hefei , Anhui 230031 , PR China
| | - Zhijun Liu
- National Facility for Protein Science in Shanghai, ZhangJiang Lab, Shanghai Advanced Research Institute , Chinese Academy of Sciences , Shanghai , 201210 , PR China
| | - Xiaogang Niu
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , PR China
| | - Gilbert Nshogoza
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences , University of Science and Technology of China , Hefei , Anhui 230027 , PR China
| | - Jiahai Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences , University of Science and Technology of China , Hefei , Anhui 230027 , PR China
| | - Jihui Wu
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences , University of Science and Technology of China , Hefei , Anhui 230027 , PR China
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) , Nankai University , Tianjin , 300071 , PR China
| | - Wei He
- Department of Pharmacology and Pharmaceutical Sciences, School of Medicine, Tsinghua-Peking Joint Center for Life Sciences , Tsinghua University , Beijing , 100084 , PR China
| | - Rongsheng Ma
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences , University of Science and Technology of China , Hefei , Anhui 230027 , PR China
| | - Daiwen Yang
- Department of Biological Sciences , National University of Singapore , Singapore , 117543 , Singapore
| | - Ke Ruan
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences , University of Science and Technology of China , Hefei , Anhui 230027 , PR China
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17
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Schlagnitweit J, Steiner E, Karlsson H, Petzold K. Efficient Detection of Structure and Dynamics in Unlabeled RNAs: The SELOPE Approach. Chemistry 2018; 24:6067-6070. [PMID: 29504639 PMCID: PMC5947647 DOI: 10.1002/chem.201800992] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Indexed: 01/10/2023]
Abstract
The knowledge of structure and dynamics is crucial to explain the function of RNAs. While nuclear magnetic resonance (NMR) is well suited to probe these for complex biomolecules, it requires expensive, isotopically labeled samples, and long measurement times. Here we present SELOPE, a new robust, proton-only NMR method that allows us to obtain site-specific overview of structure and dynamics in an entire RNA molecule using an unlabeled sample. SELOPE simplifies assignment and allows for cost-effective screening of the response of nucleic acids to physiological changes (e.g. ion concentration) or screening of drugs in a high throughput fashion. This single technique allows us to probe an unprecedented range of exchange time scales (the whole μs to ms motion range) with increased sensitivity, surpassing all current experiments to detect chemical exchange. For the first time we could describe an RNA excited state using an unlabeled RNA.
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Affiliation(s)
- Judith Schlagnitweit
- Department of Medical Biochemistry and BiophysicsKarolinska Institute17177StockholmSweden
| | - Emilie Steiner
- Department of Medical Biochemistry and BiophysicsKarolinska Institute17177StockholmSweden
| | - Hampus Karlsson
- Department of Medical Biochemistry and BiophysicsKarolinska Institute17177StockholmSweden
| | - Katja Petzold
- Department of Medical Biochemistry and BiophysicsKarolinska Institute17177StockholmSweden
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18
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Khirich G, Holliday MJ, Lin JC, Nandy A. Measurement and Characterization of Hydrogen-Deuterium Exchange Chemistry Using Relaxation Dispersion NMR Spectroscopy. J Phys Chem B 2018; 122:2368-2378. [PMID: 29376350 DOI: 10.1021/acs.jpcb.7b10849] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
One-dimensional heteronuclear relaxation dispersion NMR spectroscopy at 13C natural abundance successfully characterized the dynamics of the hydrogen-deuterium exchange reaction occurring at the Nε position in l-arginine by monitoring Cδ in varying amounts of D2O. A small equilibrium isotope effect was observed and quantified, corresponding to ΔG = -0.14 kcal mol-1. A bimolecular rate constant of kD = 5.1 × 109 s-1 M-1 was determined from the pH*-dependence of kex (where pH* is the direct electrode reading of pH in 10% D2O and kex is the nuclear spin exchange rate constant), consistent with diffusion-controlled kinetics. The measurement of ΔG serves to bridge the millisecond time scale lifetimes of the detectable positively charged arginine species with the nanosecond time scale lifetime of the nonobservable low-populated neutral arginine intermediate species, thus allowing for characterization of the equilibrium lifetimes of the various arginine species in solution as a function of fractional solvent deuterium content. Despite the system being in fast exchange on the chemical shift time scale, the magnitude of the secondary isotope shift due to the exchange reaction at Nε was accurately measured to be 0.12 ppm directly from curve-fitting D2O-dependent dispersion data collected at a single static field strength. These results indicate that relaxation dispersion NMR spectroscopy is a robust and general method for studying base-catalyzed hydrogen-deuterium exchange chemistry at equilibrium.
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Affiliation(s)
- Gennady Khirich
- Protein Analytical Chemistry, ‡Early Discovery Biochemistry, and §Late Stage Pharmaceutical Development, Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States
| | - Michael J Holliday
- Protein Analytical Chemistry, ‡Early Discovery Biochemistry, and §Late Stage Pharmaceutical Development, Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States
| | - Jasper C Lin
- Protein Analytical Chemistry, ‡Early Discovery Biochemistry, and §Late Stage Pharmaceutical Development, Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States
| | - Aditya Nandy
- Protein Analytical Chemistry, ‡Early Discovery Biochemistry, and §Late Stage Pharmaceutical Development, Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States
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19
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Reddy JG, Pratihar S, Ban D, Frischkorn S, Becker S, Griesinger C, Lee D. Simultaneous determination of fast and slow dynamics in molecules using extreme CPMG relaxation dispersion experiments. JOURNAL OF BIOMOLECULAR NMR 2018; 70:1-9. [PMID: 29188417 DOI: 10.1007/s10858-017-0155-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 11/20/2017] [Indexed: 06/07/2023]
Abstract
Molecular dynamics play a significant role in how molecules perform their function. A critical method that provides information on dynamics, at the atomic level, is NMR-based relaxation dispersion (RD) experiments. RD experiments have been utilized for understanding multiple biological processes occurring at micro-to-millisecond time, such as enzyme catalysis, molecular recognition, ligand binding and protein folding. Here, we applied the recently developed high-power RD concept to the Carr-Purcell-Meiboom-Gill sequence (extreme CPMG; E-CPMG) for the simultaneous detection of fast and slow dynamics. Using a fast folding protein, gpW, we have shown that previously inaccessible kinetics can be accessed with the improved precision and efficiency of the measurement by using this experiment.
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Affiliation(s)
- Jithender G Reddy
- Department for NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
- NMR & Structural Chemistry Division, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500007, India
| | - Supriya Pratihar
- Department for NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - David Ban
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St, Louisville, KY, 40202, USA
| | - Sebastian Frischkorn
- Department for NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Stefan Becker
- Department for NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Christian Griesinger
- Department for NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Donghan Lee
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St, Louisville, KY, 40202, USA.
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20
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Zawadzka-Kazimierczuk A, Somlyay M, Kaehlig H, Iakobson G, Beier P, Konrat R. 19F multiple-quantum coherence NMR spectroscopy for probing protein–ligand interactions. RSC Adv 2018; 8:40687-40692. [PMID: 35557931 PMCID: PMC9091488 DOI: 10.1039/c8ra09296f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 01/25/2019] [Accepted: 11/28/2018] [Indexed: 11/23/2022] Open
Abstract
A new 19F NMR method is presented which can be used to detect weak protein binding of small molecules with up to mM affinity. The method capitalizes on the synthetic availability of unique SF5 containing compounds and the generation of five-quantum coherences (5QC). Given the high sensitivity of 5QC relaxation to exchange events (i.e. reversible protein binding) fragments which bind to the target with weak affinity can be identified. The utility of the method in early stage drug discovery programs is demonstrated with applications to two model proteins, the neurotoxic NGAL and the prominent tumor target β-catenin. An NMR experiment is presented that allows identification of weak binders typically found in early stages of drug discovery programs.![]()
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Affiliation(s)
- Anna Zawadzka-Kazimierczuk
- Department of Structural and Computational Biology
- Max F. Perutz Laboratories
- University of Vienna
- A-1030 Vienna
- Austria
| | - Mate Somlyay
- Department of Structural and Computational Biology
- Max F. Perutz Laboratories
- University of Vienna
- A-1030 Vienna
- Austria
| | - Hanspeter Kaehlig
- Institute of Organic Chemistry
- University of Vienna
- A-1090 Vienna
- Austria
| | - George Iakobson
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
- 160 00 Prague
- Czech Republic
| | - Petr Beier
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
- 160 00 Prague
- Czech Republic
| | - Robert Konrat
- Department of Structural and Computational Biology
- Max F. Perutz Laboratories
- University of Vienna
- A-1030 Vienna
- Austria
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21
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Trigo-Mouriño P, Griesinger C, Lee D. Label-free NMR-based dissociation kinetics determination. JOURNAL OF BIOMOLECULAR NMR 2017; 69:229-235. [PMID: 29143948 DOI: 10.1007/s10858-017-0150-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 11/03/2017] [Indexed: 06/07/2023]
Abstract
Understanding the dissociation of molecules is the basis to modulate interactions of biomedical interest. Optimizing drugs for dissociation rates is found to be important for their efficacy, selectivity, and safety. Here, we show an application of the high-power relaxation dispersion (RD) method to the determination of the dissociation rates of weak binding ligands from receptors. The experiment probes proton RD on the ligand and, therefore, avoids the need for any isotopic labeling. The large ligand excess eases the detection significantly. Importantly, the use of large spin-lock fields allows the detection of faster dissociation rates than other relaxation approaches. Moreover, this experimental approach allows to access directly the off-rate of the binding process without the need for analyzing a series of samples with increasing ligand saturation. The validity of the method is shown with small molecule interactions using two macromolecules, bovine serum albumin and tubulin heterodimers.
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Affiliation(s)
- Pablo Trigo-Mouriño
- Department of NMR-Based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Christian Griesinger
- Department of NMR-Based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Donghan Lee
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY, 40202, USA.
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