1
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Szabó CL, Sebák F, Bodor A. Monitoring Protein Global and Local Parameters in Unfolding and Binding Studies: The Extended Applicability of the Diffusion Coefficient─Molecular Size Empirical Relations. Anal Chem 2022; 94:7885-7891. [PMID: 35617314 DOI: 10.1021/acs.analchem.2c00481] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Protein unfolding and denaturation are main issues in biochemical and pharmaceutical research. Using a global parameter, the translational diffusion coefficient D, folded, unfolded, and intrinsically disordered proteins of a given molar mass M can be distinguished based on their distinct hydrodynamic properties. For broader applications, we provide generalized, PFG-NMR-based empirical D-M relations validated at different temperatures and ready to use with the corresponding corrections in different media. We demonstrate that these relations enable a more accurate molecular mass determination and show fewer potential errors than those of the common methods based on small-molecular diffusion standards. We monitor unfolding of three model proteins using 8 M urea and dimethyl sulfoxide (DMSO)-water mixtures as denaturing agents, highlighting the effect of disulfide bonds. Denaturation in 8 M urea is pH-dependent; in addition, for proteins with highly stable disulfide bonds, a reducing agent (TCEP) is required to achieve complete unfolding. Regarding the effect of local parameters, we show that at low DMSO concentrations─common conditions in pharmaceutical binding studies─the PFG-NMR-derived global parameters are not significantly affected. Still, the atomic environments can change, and the bound solvent molecule can inhibit the binding of a partner molecule. Using proteins with natural isotopic abundance, this effect can be proven by fast 1H-15N 2D correlation spectra. Our results enable fast and easy estimation of protein molecular mass and the degree of folding in various media; moreover, the effect of the cosolvent on the atomic-level structure can be traced without the need of isotope labeling.
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Affiliation(s)
- Csenge Lilla Szabó
- Institute of Chemistry, Analytical and BioNMR Laboratory, Eötvös Loránd University, Pázmány Péter sétány 1/a, Budapest 1117, Hungary.,Hevesy György PhD School of Chemistry, Eötvös Loránd University, Pázmány Péter sétány 1/a, Budapest 1117, Hungary
| | - Fanni Sebák
- Institute of Chemistry, Analytical and BioNMR Laboratory, Eötvös Loránd University, Pázmány Péter sétány 1/a, Budapest 1117, Hungary
| | - Andrea Bodor
- Institute of Chemistry, Analytical and BioNMR Laboratory, Eötvös Loránd University, Pázmány Péter sétány 1/a, Budapest 1117, Hungary
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2
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Mukherjee D, Trigo-Mouriño P, Jiang Y, Nowak T, Shchurik V, Adpressa DA, Louie MT, Reynolds SR, Hohn MJ, Al-Sayah MA, Pirrone GF, Makarov AA. Rapid antibody conformational screening by matrix assisted laser desorption ionization hydrogen-deuterium exchange mass spectrometry. J Sep Sci 2022; 45:2055-2063. [PMID: 35108448 DOI: 10.1002/jssc.202100986] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/25/2022] [Accepted: 01/29/2022] [Indexed: 11/06/2022]
Abstract
Recent advances in the field of cancer biology have accelerated the discovery and development of novel biopharmaceuticals. At the forefront of these drug development efforts are high-throughput screening, compressed timelines and limited sample quantities, all characteristic of the discovery space. To meet program targets, large numbers of protein variants must be produced, screened, and characterized, presenting a daunting analytical challenge. Additionally, higher-order structure is paramount for protein function and must be monitored as a critical quality attribute. Matrix Assisted Laser Desorption Ionization MS has been utilized as an ultra-fast, automatable, sample-sparing analytical tool for biomolecules. Our group has published applications integrating Hydrogen-Deuterium Exchange MS with Matrix Assisted Laser Desorption Ionization MS for the rapid conformational characterization of small proteins, the current work expands this application to monoclonal and bi-specific antibodies. This study demonstrates the ability of the methodology Matrix Assisted Laser Desorption Ionization Hydrogen-Deuterium Exchange MS to detect conformational differences between bi-specific antibodies from different expression host. These conformational differences were validated by orthogonal techniques including Circular Dichroism, Nuclear Magnetic Resonance and Size-Exclusion Chromatography Hydrogen-Deuterium Exchange MS. This work demonstrates the utility of applying the developed methodology as a rapid conformational screening tool to triage samples for further analytical characterization. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Debopreeti Mukherjee
- Merck & Co. Inc., MRL, Analytical Research & Development, Boston, MA, 02115, USA
| | - Pablo Trigo-Mouriño
- Merck & Co. Inc., MRL, Analytical Research & Development, Boston, MA, 02115, USA
| | - Yuan Jiang
- Merck & Co. Inc., MRL, Analytical Research & Development, Boston, MA, 02115, USA
| | - Timothy Nowak
- Merck & Co. Inc., MRL, Analytical Research & Development, Boston, MA, 02115, USA
| | - Vladimir Shchurik
- Merck & Co. Inc., MRL, Analytical Research & Development, Boston, MA, 02115, USA
| | - Donovon A Adpressa
- Merck & Co. Inc., MRL, Analytical Research & Development, Boston, MA, 02115, USA
| | | | | | - Michael J Hohn
- Merck & Co. Inc., MRL, Analytical Research & Development, Boston, MA, 02115, USA
| | | | - Gregory F Pirrone
- Merck & Co. Inc., MRL, Analytical Research & Development, Boston, MA, 02115, USA
| | - Alexey A Makarov
- Merck & Co. Inc., MRL, Analytical Research & Development, Boston, MA, 02115, USA
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3
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Falk BT, Liang Y, McCoy MA. Diffusion Profiling of Therapeutic Proteins by Using Solution NMR Spectroscopy. Chembiochem 2019; 20:896-899. [PMID: 30515922 DOI: 10.1002/cbic.201800631] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Indexed: 11/10/2022]
Abstract
Characterizing changes to structure and behavior is an important aspect of therapeutic protein development. NMR spectroscopy is well suited to study interactions and higher-order structure that could impact biological function and safety. We used NMR diffusion methods to describe the overall behavior of proteins in solution by defining a "diffusion profile" that captures the complexities in diffusion behavior. Diffusion profiles offer a simple means to interpret protein solution behavior as a distribution of sizes and association states. As a characterization method, diffusion profiling is well suited to complement and augment traditional biophysical and NMR methods to probe the solution behavior of therapeutic proteins.
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Affiliation(s)
- Bradley T Falk
- Mass Spectrometry and Biophysics, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033, USA
| | - Yingkai Liang
- Pharmaceutical Sciences, Merck & Co., Inc., 770 Sumneytown Pike, West Point, PA, 19486, USA
| | - Mark A McCoy
- Mass Spectrometry and Biophysics, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033, USA
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4
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Dudás EF, Bodor A. Quantitative, Diffusion NMR Based Analytical Tool To Distinguish Folded, Disordered, and Denatured Biomolecules. Anal Chem 2019; 91:4929-4933. [DOI: 10.1021/acs.analchem.8b05617] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Erika F. Dudás
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter sétány 1/a, Budapest 1117, Hungary
| | - Andrea Bodor
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter sétány 1/a, Budapest 1117, Hungary
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5
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Jütten L, Ramírez-Gualito K, Weilhard A, Albrecht B, Cuevas G, Fernández-Alonso MD, Jiménez-Barbero J, Schlörer NE, Diaz D. Exploring the Role of Solvent on Carbohydrate-Aryl Interactions by Diffusion NMR-Based Studies. ACS OMEGA 2018; 3:536-543. [PMID: 31457911 PMCID: PMC6641296 DOI: 10.1021/acsomega.7b01630] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 12/28/2017] [Indexed: 05/26/2023]
Abstract
Carbohydrate-protein interactions play an important role in many molecular recognition processes. An exquisite combination of multiple factors favors the interaction of the receptor with one specific type of sugar, whereas others are excluded. Stacking CH-aromatic interactions within the binding site provide a relevant contribution to the stabilization of the resulting sugar-protein complex. Being experimentally difficult to detect and analyze, the key CH-π interaction features have been very often dissected using a variety of techniques and simple model systems. In the present work, diffusion NMR spectroscopy has been employed to separate the components of sugar mixtures in different solvents on the basis of their differential ability to interact through CH-π interactions with one particular aromatic cosolute in solution. The experimental data show that the properties of the solvent did also influence the diffusion behavior of the sugars present in the mixture, inhibiting or improving their separation. Overall, the results showed that, for the considered monosaccharide derivatives, their diffusion coefficient values and, consequently, their apparent molecular sizes and/or shapes depend on the balance between solute/cosolute as well as solute/solvent interactions. Thus, in certain media and in the presence of the aromatic cosolute, the studied saccharides that are more suited to display CH-π interactions exhibited a lower diffusion coefficient than the noncomplexing sugars in the mixture. However, when dissolved in another medium, the interaction with the solvent strongly competes with that of the aromatic cosolute.
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Affiliation(s)
- Linda Jütten
- Department
für Chemie, NMR-Abteilung, Universität
zu Köln, Greinstr.
4, 50939 Köln, Germany
| | - Karla Ramírez-Gualito
- Centro
de Nanociencias y Micro y Nanotecnología, Instituto Politécnico Nacional, Avenida Luis Enrique Erro S/N, Unidad Profesional
Adolfo López Mateos, Zacatenco, C.P. 07738 Ciudad de México, México
| | - Andreas Weilhard
- Department
für Chemie, NMR-Abteilung, Universität
zu Köln, Greinstr.
4, 50939 Köln, Germany
| | - Benjamin Albrecht
- Department
für Chemie, NMR-Abteilung, Universität
zu Köln, Greinstr.
4, 50939 Köln, Germany
| | - Gabriel Cuevas
- Instituto
de Química, Universidad Nacional Autónoma de México,
Circuito Exterior, Ciudad Universitaria, Delegación Coyoacán, C.P. 04510 Ciudad de México, México
| | | | - Jesús Jiménez-Barbero
- Centro
de Investigaciones Biológicas (CIB-CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
- CIC
bioGUNE, Science and
Technology Park bld 801 A, 48160 Derio, Spain
- Basque Foundation
for Science, Ikerbasque, Maria Diaz de Haro 3, 48013 Bilbao, Spain
- Department
of Organic Chemistry II, Faculty of Science & Technology, University of the Basque Country, 48940 Leioa, Spain
| | - Nils E. Schlörer
- Department
für Chemie, NMR-Abteilung, Universität
zu Köln, Greinstr.
4, 50939 Köln, Germany
| | - Dolores Diaz
- Department
für Chemie, NMR-Abteilung, Universität
zu Köln, Greinstr.
4, 50939 Köln, Germany
- Centro
de Investigaciones Biológicas (CIB-CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
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6
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Bleuler-Martinez S, Stutz K, Sieber R, Collot M, Mallet JM, Hengartner M, Schubert M, Varrot A, Künzler M. Dimerization of the fungal defense lectin CCL2 is essential for its toxicity against nematodes. Glycobiology 2017; 27:486-500. [PMID: 27980000 DOI: 10.1093/glycob/cww113] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 11/09/2016] [Indexed: 11/12/2022] Open
Abstract
Lectins are used as defense effector proteins against predators, parasites and pathogens by animal, plant and fungal innate defense systems. These proteins bind to specific glycoepitopes on the cell surfaces and thereby interfere with the proper cellular functions of the various antagonists. The exact cellular toxicity mechanism is in many cases unclear. Lectin CCL2 of the mushroom Coprinopsis cinerea was previously shown to be toxic for Caenorhabditis elegans and Drosophila melanogaster. This toxicity is dependent on a single, high-affinity binding site for the trisaccharide GlcNAc(Fucα1,3)β1,4GlcNAc, which is a hallmark of nematode and insect N-glycan cores. The carbohydrate-binding site is located at an unusual position on the protein surface when compared to other β-trefoil lectins. Here, we show that CCL2 forms a compact dimer in solution and in crystals. Substitution of two amino acid residues at the dimer interface, R18A and F133A, interfered with dimerization of CCL2 and reduced toxicity but left carbohydrate-binding unaffected. These results, together with the positioning of the two carbohydrate-binding sites on the surface of the protein dimer, suggest that crosslinking of N-glycoproteins on the surface of intestinal cells of invertebrates is a crucial step in the mechanism of CCL2-mediated toxicity. Comparisons of the number and positioning of carbohydrate-binding sites among different dimerizing fungal β-trefoil lectins revealed a considerable variability in the carbohydrate-binding patterns of these proteins, which are likely to correlate with their respective functions.
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Affiliation(s)
| | - Katrin Stutz
- Institute of Molecular Life Sciences, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Ramon Sieber
- Institute of Microbiology, ETH Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Mayeul Collot
- Laboratoire des Biomolécules, UPMC Université Paris 06, Ecole Normale Supérieure, Paris, France
| | - Jean-Maurice Mallet
- Laboratoire des Biomolécules, UPMC Université Paris 06, Ecole Normale Supérieure, Paris, France
| | - Michael Hengartner
- Institute of Molecular Life Sciences, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Mario Schubert
- Institute of Molecular Biology and Biophysics, ETH Zürich, Schafmattstr. 20, 8093 Zürich, Switzerland.,Department of Molecular Biology, University of Salzburg, Billrothstrasse 11, 5020 Salzburg, Austria
| | - Annabelle Varrot
- CERMAV, UPR5301, CNRS and Université Grenoble Alpes, 38041 Grenoble, France
| | - Markus Künzler
- Institute of Microbiology, ETH Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
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7
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Abstract
Optimization of Diffusion Ordered NMR Spectroscopy (DOSY) parameters for the improved and extended analysis of polymers.
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Affiliation(s)
- Patrick Groves
- Department of Biomedicinal Chemistry
- University of Gdansk
- 80-308 Gdansk
- Poland
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8
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Díaz D, Canales-Mayordomo A, Cañada FJ, Jiménez-Barbero J. Solution conformation of carbohydrates: a view by using NMR assisted by modeling. Methods Mol Biol 2015; 1273:261-87. [PMID: 25753717 DOI: 10.1007/978-1-4939-2343-4_19] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Structural elucidation of complex carbohydrates in solution is not a trivial task. From the NMR view point, the limited chemical shift dispersion of sugar NMR spectra demands the combination of a variety of NMR techniques as well as the employment of molecular modeling methods. Herein, a general protocol for assignment of resonances and determination of inter-proton distances within the saccharides by homonuclear and heteronuclear experiments (i.e., (1)H and (13)C) is described. In addition, several computational tools and procedures for getting a final ensemble of geometries that represent the structure in solution are presented.
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Affiliation(s)
- Dolores Díaz
- Centro de Investigaciones Biológicas, CIB-CSIC, Madrid, Spain
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9
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Structural studies of novel glycoconjugates from polymerized allergens (allergoids) and mannans as allergy vaccines. Glycoconj J 2015; 33:93-101. [PMID: 26603537 PMCID: PMC4722057 DOI: 10.1007/s10719-015-9640-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 11/15/2015] [Accepted: 11/18/2015] [Indexed: 10/26/2022]
Abstract
Immunotherapy for treating IgE-mediated allergies requires high doses of the corresponding allergen. This may result in undesired side effects and, to avoid them, hypoallergenic allergens (allergoids) polymerized with glutaraldehyde are commonly used. Targeting allergoids to dendritic cells to enhance cell uptake may result in a more effective immunotherapy. Allergoids coupled to yeast mannan, as source of polymannoses, would be suitable for this purpose, since mannose-binding receptors are expressed on these cells. Conventional conjugation procedures of mannan to proteins use oxidized mannan to release reactive aldehydes able to bind to free amino groups in the protein; yet, allergoids lack these latter because their previous treatment with glutaraldehyde. The aim of this study was to obtain allergoids conjugated to mannan by an alternative approach based on just glutaraldehyde treatment, taking advantage of the mannoprotein bound to the polymannose backbone. Allergoid-mannan glycoconjugates were produced in a single step by treating with glutaraldehyde a defined mixture of allergens derived from Phleum pratense grass pollen and native mannan (non-oxidized) from Saccharomyces cerevisae. Analytical and structural studies, including 2D-DOSY and (1)H-(13)C HSQC nuclear magnetic resonance spectra, demonstrated the feasibility of such an approach. The glycoconjugates obtained were polymers of high molecular weight showing a higher stability than the native allergen or the conventional allergoid without mannan. The allergoid-mannan glycoconjugates were hypoallergenic as detected by the IgE reactivity with sera from grass allergic patients, even with lower reactivity than conventional allergoid without mannan. Thus, stable hypoallergenic allergoids conjugated to mannan suitable for using in immunotherapy can be achieved using glutaraldehyde. In contrast to mannan oxidation, the glutaraldehyde approach allows to preserve mannoses with their native geometry, which may be functionally important for its receptor-mediated recognition.
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10
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van de Weerd R, Berbís MA, Sparrius M, Maaskant JJ, Boot M, Paauw NJ, de Vries N, Boon L, Baba O, Cañada FJ, Geurtsen J, Jiménez-Barbero J, Appelmelk BJ. A murine monoclonal antibody to glycogen: characterization of epitope-fine specificity by saturation transfer difference (STD) NMR spectroscopy and its use in mycobacterial capsular α-glucan research. Chembiochem 2015; 16:977-89. [PMID: 25766777 DOI: 10.1002/cbic.201402713] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Indexed: 12/12/2022]
Abstract
Mycobacterium tuberculosis, the causative agent of tuberculosis (TB), is a major pathogen responsible for 1.5 million deaths annually. This bacterium is characterized by a highly unusual and impermeable cell envelope, which plays a key role in mycobacterial survival and virulence. Although many studies have focused on the composition and functioning of the mycobacterial cell envelope, the capsular α-glucan has received relatively minor attention. Here we show that a murine monoclonal antibody (Mab) directed against glycogen cross-reacts with mycobacterial α-glucans, polymers of α(1-4)-linked glucose residues with α(1-6)-branch points. We identified the Mab epitope specificity by saturation transfer difference NMR and show that the α(1-4)-linked glucose residues are important in glucan-Mab interaction. The minimal epitope is formed by (linear) maltotriose. Notably, a Mycobacterium mutant lacking the branching enzyme GlgB does not react with the Mab; this suggests that the α(1-6)-branches form part of the epitope. These seemingly conflicting data can be explained by the fact that in the mutant the linear form of the α-glucan (amylose) is insoluble. This Mab was subsequently used to develop several techniques helpful in capsular α-glucan research. By using a capsular glucan-screening methodology based on this Mab we were able to identify several unknown genes involved in capsular α-glucan biogenesis. Additionally, we developed two methods for the detection of capsular α-glucan levels. This study therefore opens new ways to study capsular α-glucan and to identify possible targets for further research.
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Affiliation(s)
- Robert van de Weerd
- Department of Medical Microbiology and Infection Control, VU University Medical Center, Van der Boechorststraat 7, 1081 BT Amsterdam (The Netherlands)
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11
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Stötzel S, Schurink M, Wienk H, Siebler U, Burg-Roderfeld M, Eckert T, Kulik B, Wechselberger R, Sewing J, Steinmeyer J, Oesser S, Boelens R, Siebert HC. Molecular Organization of Various Collagen Fragments as Revealed by Atomic Force Microscopy and Diffusion-Ordered NMR Spectroscopy. Chemphyschem 2012; 13:3117-25. [DOI: 10.1002/cphc.201200284] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Indexed: 12/22/2022]
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12
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Reinstein O, Neves MAD, Saad M, Boodram SN, Lombardo S, Beckham SA, Brouwer J, Audette GF, Groves P, Wilce MCJ, Johnson PE. Engineering a structure switching mechanism into a steroid-binding aptamer and hydrodynamic analysis of the ligand binding mechanism. Biochemistry 2011; 50:9368-76. [PMID: 21942676 DOI: 10.1021/bi201361v] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The steroid binding mechanism of a DNA aptamer was studied using isothermal titration calorimetry (ITC), NMR spectroscopy, quasi-elastic light scattering (QELS), and small-angle X-ray spectroscopy (SAXS). Binding affinity determination of a series of steroid-binding aptamers derived from a parent cocaine-binding aptamer demonstrates that substituting a GA base pair with a GC base pair governs the switch in binding specificity from cocaine to the steroid deoxycholic acid (DCA). Binding of DCA to all aptamers is an enthalpically driven process with an unfavorable binding entropy. We engineered into the steroid-binding aptamer a ligand-induced folding mechanism by shortening the terminal stem by two base pairs. NMR methods were used to demonstrate that there is a transition from a state where base pairs are formed in one stem of the free aptamer, to where three stems are formed in the DCA-bound aptamer. The ability to generate a ligand-induced folding mechanism into a DNA aptamer architecture based on the three-way junction of the cocaine-binding aptamer opens the door to obtaining a series of aptamers all with ligand-induced folding mechanisms but triggered by different ligands. Hydrodynamic data from diffusion NMR spectroscopy, QELS, and SAXS show that for the aptamer with the full-length terminal stem there is a small amount of structure compaction with DCA binding. For ligand binding by the short terminal stem aptamer, we propose a binding mechanism where secondary structure forms upon DCA binding starting from a free structure where the aptamer exists in a compact form.
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Affiliation(s)
- Oren Reinstein
- Department of Chemistry, York University, Toronto, Ontario, Canada M3J 1P3
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13
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Kagan G, Li W, Li D, Hopson R, Williard PG. Characterization of dimeric chiral lithium amide structures derived from N-isopropyl-O- triisopropylsilyl valinol. J Am Chem Soc 2011; 133:6596-602. [PMID: 21486016 DOI: 10.1021/ja109041z] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The dimeric structure is characterized for a chiral amide base complex consisting of an (S)-N-isopropyl-O-triisopropylsilyl valinol ligand and lithium. The complex is characterized by a variety of NMR techniques, including multinuclear one- and two-dimensional NMR experiments and diffusion-ordered NMR spectroscopy (DOSY) as well as diffusion coefficient-formula weight (D-fw) correlation analyses. Spartan calculations are presented which support the structural assignment. This structural characterization leads to an explanation of the behavior and the reactivity of these complexes in solution.
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Affiliation(s)
- Gerald Kagan
- Department of Chemistry, Brown University, 324 Brook Street, Providence, Rhode Island 02912, USA
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14
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Li D, Kagan G, Hopson R, Williard PG. Formula weight prediction by internal reference diffusion-ordered NMR spectroscopy (DOSY). J Am Chem Soc 2010; 131:5627-34. [PMID: 19323518 DOI: 10.1021/ja810154u] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Formula weight (FW) information is important to characterize the composition, aggregation number, and solvation state of reactive intermediates and organometallic complexes. We describe an internal reference correlated DOSY method for calculating the FW of unknown species in different solvents with different concentrations. Examples for both the small molecule (DIPA) and the organometallic complex (aggregate 1) yield excellent correlations. We also found the relative diffusion rate is inversely proportional to the viscosity change of the solution, which is consistent with the theoretical Stokes-Einstein equation. The accuracy of the least-squares linear prediction r(2) and the percentage difference of FW prediction are directly related to the density change; greater accuracy was observed with decreasing density. We also discuss the guidelines and other factors for successful application of this internal reference correlated DOSY method. This practical method can be conveniently modified and applied to the characterization of other unknown molecules or complexes.
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Affiliation(s)
- Deyu Li
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, USA
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15
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Groves P, Webba da Silva M. Rapid stoichiometric analysis of G-quadruplexes in solution. Chemistry 2010; 16:6451-3. [PMID: 20449855 DOI: 10.1002/chem.200901248] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Patrick Groves
- Department of Biological Chemistry, Instituto de Tecnologia Química e Biológica, Address 2 Av. da República (EAN), 2781-901 Oeiras, Portugal
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16
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Li W, Kagan G, Yang H, Cai C, Hopson R, Sweigart DA, Williard PG. Physically Separated References for Diffusion Coefficient-Formula Weight (D-FW) Analysis of Diffusion-Ordered NMR Spectroscopy (DOSY) in Water. Org Lett 2010; 12:2698-701. [DOI: 10.1021/ol100686e] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Weibin Li
- Department of Chemistry, Brown University Providence, Rhode Island 02912
| | - Gerald Kagan
- Department of Chemistry, Brown University Providence, Rhode Island 02912
| | - Huan Yang
- Department of Chemistry, Brown University Providence, Rhode Island 02912
| | - Chen Cai
- Department of Chemistry, Brown University Providence, Rhode Island 02912
| | - Russell Hopson
- Department of Chemistry, Brown University Providence, Rhode Island 02912
| | - Dwight A. Sweigart
- Department of Chemistry, Brown University Providence, Rhode Island 02912
| | - Paul G. Williard
- Department of Chemistry, Brown University Providence, Rhode Island 02912
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17
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Ribeiro JP, Palczewska M, André S, Cañada FJ, Gabius HJ, Jiménez-Barbero J, Mellström B, Naranjo JR, Scheffers DJ, Groves P. Diffusion nuclear magnetic resonance spectroscopy detects substoichiometric concentrations of small molecules in protein samples. Anal Biochem 2010; 396:117-23. [DOI: 10.1016/j.ab.2009.09.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2009] [Revised: 08/21/2009] [Accepted: 09/01/2009] [Indexed: 10/20/2022]
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18
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Oda Y, Matsuda S, Yamanoi T, Murota A, Katsuraya K. Identification of the inclusion complexation between phenyl β-d-(13C6)glucopyranoside and α-cyclodextrin using 2D 1H or 13C DOSY spectrum. Supramol Chem 2009. [DOI: 10.1080/10610270802709345] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
| | | | | | - Akihiko Murota
- b Department of Applied Chemistry , School of Science and Technology, Meiji University , Kanagawa, Japan
| | - Kaname Katsuraya
- c Department of Human Ecology , Wayo Women's University , Chiba, Japan
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Vermillion K, Price NPJ. Stable isotope-enhanced two- and three-dimensional diffusion ordered 13C NMR spectroscopy (SIE-DOSY 13C NMR). JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2009; 198:209-214. [PMID: 19303336 DOI: 10.1016/j.jmr.2009.02.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2008] [Revised: 02/20/2009] [Accepted: 02/20/2009] [Indexed: 05/27/2023]
Abstract
The feasibility of obtaining high quality homonuclear or heteronuclear diffusion-ordered (13)C NMR data is shown to be greatly improved by using (13)C isotopically-enriched samples. Stable isotope-enhanced diffusion ordered (SIE-DOSY) (13)C NMR has been applied to (13)C-enriched carbohydrates, and has been used to determine diffusion coefficients for pentose and hexose monosaccharides, and a disaccharide and trisaccharide. These 2D spectra were obtained with as little as 8 min of acquisition time. Fully resolved 3D DOSY-HMQC NMR spectra of [U-(13)C]xylose, [U-(13)C]glucose, and [1-(13)C(gal)]lactose were obtained in 5h. Sample derivatization with [carbonyl-(13)C]acetate (peracetylation) extends the usefulness of the technique to included non-labeled sugars; the (13)C-carbonyl - carbohydrate ring proton (1)H-(13)C correlations also provide additional structural information, as shown for the 3-D DOSY-HMQC analysis of a mixture of maltotriose and lactose per-[carbonyl-(13)C]acetates.
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Affiliation(s)
- Karl Vermillion
- New Crops and Processing Technology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, United States Department of Agriculture, Peoria, IL 61604, USA.
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Santos JI, Carvalho de Souza A, Cañada FJ, Martín-Santamaría S, Kamerling JP, Jiménez-Barbero J. Assessing carbohydrate-carbohydrate interactions by NMR spectroscopy: the trisaccharide epitope from the marine sponge Microciona prolifera. Chembiochem 2009; 10:511-9. [PMID: 19123195 DOI: 10.1002/cbic.200800548] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
WEAK RECOGNITION PROCESSES: Weak calcium-mediated carbohydrate-carbohydrate interactions have been detected by DOSY and TRNOESY NMR methods by employing a gold glyconanoparticle as a multivalent system. In addition, 3D models of trisaccharide-Ca(II)-trisaccharide complexes based on results from molecular dynamics simulations are proposed. Diffusion-ordered NMR spectroscopy (DOSY-NMR) and TR-NOESY-NMR experiments are used to detect ligand binding to macromolecular receptors. These techniques have been applied to detect weak carbohydrate-carbohydrate self-recognition in solution, making use of sugar-decorated gold nanoparticles as the "macromolecule" and the same carbohydrate as the ligand. Changes in the diffusion coefficient of the free carbohydrate in the presence of the glyconanoparticle (only with Ca(II) ions in the sample solution), as well as changes in the sign of the sugar NOE peaks--positive for the free sugar (in the presence or absence of Ca(II)) and negative for the sugar only in the simultaneous presence of the glyconanoparticle and Ca(II) ions--have been taken as proof of weak Ca(II)-mediated carbohydrate-carbohydrate interactions in solution. Although different methods such as SPR, TEM, and AFM have been used in the past to detect carbohydrate-carbohydrate interactions with the aid of gold nanoparticles and gold selfassembled monolayers, they are restricted to high-affinity ranges. The methods used in this study allow expansion of the number of techniques to tackle this relevant biological problem, also for approaching ligand-receptor interactions below the high-affinity range. Additionally, 3D models of trisaccharide-Ca(II)-trisaccharide complexes based on results from molecular dynamics simulations are proposed.
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Li D, Hopson R, Li W, Liu J, Williard PG. 13C INEPT diffusion-ordered NMR spectroscopy (DOSY) with internal references. Org Lett 2008; 10:909-11. [PMID: 18251549 PMCID: PMC3220947 DOI: 10.1021/ol703039v] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
13C INEPT Diffusion-ordered NMR spectroscopy (DOSY) with an internal reference system was developed to study the aggregation state of THF-solvated LDA dimeric complex. Six components are clearly identified in the diffusion dimension, and their DOSY-generated 13C INEPT spectrum slices agree extremely well with their respective INEPT spectra. The correlation between log D and log FW of the linear least-squares fit to reference points of all components is exceptionally high: (r = 0.9985).
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Affiliation(s)
- Deyu Li
- Department of Chemistry, Brown University, Providence, RI 02912 USA
| | - Russell Hopson
- Department of Chemistry, Brown University, Providence, RI 02912 USA
| | - Weibin Li
- Department of Chemistry, Brown University, Providence, RI 02912 USA
| | - Jia Liu
- Department of Chemistry, Brown University, Providence, RI 02912 USA
| | - Paul G. Williard
- Department of Chemistry, Brown University, Providence, RI 02912 USA
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22
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Ambrus A, Yang D. Diffusion-ordered nuclear magnetic resonance spectroscopy for analysis of DNA secondary structural elements. Anal Biochem 2007; 367:56-67. [PMID: 17570331 PMCID: PMC1993845 DOI: 10.1016/j.ab.2007.04.025] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2007] [Revised: 04/04/2007] [Accepted: 04/19/2007] [Indexed: 10/23/2022]
Abstract
Structure determination of secondary DNA structural elements, such as G-quadruplexes, gains an increasing importance as fundamental physiological roles are being associated with the formation of such structures in vivo. A truncated native DNA sequence generally requires further optimization to obtain a candidate with desired nuclear magnetic resonance (NMR) properties for structural analysis in solution. The optimum sequence is expected to form one dominant, stable molecular entity in solution with well-resolved NMR peaks. However, DNA sequences are prone to form structures composed of one, two, three, or four strands depending on sequence and solution conditions. The thorough characterization of the molecularity (stoichiometry and molecular weight) and appropriate solution conditions for sequences with different modifications traditionally applies analytical techniques that generally do not represent the solution conditions for NMR structure determination. Here we present the application of diffusion-ordered NMR spectroscopy as a useful analytical tool for the optimization and analysis of DNA secondary structural elements, specifically, the DNA G-quadruplex structures, including those formed in the human telomeric sequence and in the promoter regions of bcl-2 and c-myc genes.
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Affiliation(s)
- Attila Ambrus
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, AZ 85721, USA.
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Chevalier F, Lopez-Prados J, Groves P, Perez S, Martín-Lomas M, Nieto PM. Structure and dynamics of the conserved protein GPI anchor core inserted into detergent micelles. Glycobiology 2006; 16:969-80. [PMID: 16774909 DOI: 10.1093/glycob/cwl015] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
A suitable approach which combines nuclear magnetic resonance (NMR) spectroscopy and molecular dynamics (MD) simulations have been used to study the structure and the dynamics of the glycosylphosphatidylinositol (GPI) anchor Manalphal-2Manalpha1-6Manalphal -4GlcNalpha1-6myo-inositol-1-OPO(3)-sn-1,2-dimyristoylglycerol (1) incorporated into dodecylphosphatidylcholine (DPC) micelles. The results have been compared to those previously obtained for the products obtainable from (1) after phospholipase cleavage, in aqueous solution. Relaxation and diffusion NMR experiments were used to establish the formation of stable aggregates and the insertion of (1) into the micelles. MD calculations were performed including explicit water, sodium and chloride ions and using the Particle Mesh Ewald approach for the evaluation of the electrostatic energy term. The MD predicted three dimensional structure and dynamics were substantiated by nuclear overhauser effect (NOE) measurements and relaxation data. The pseudopentasaccharide structure, which was not affected by incorporation of (1) into the micelle, showed a complex dynamic behaviour with a faster relative motion at the terminal mannopyranose unit and decreased mobility close to the micelle. This motion may be better described as an oscillation relative to the membrane rather than a folding event.
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Affiliation(s)
- Franck Chevalier
- Grupo de Carbohidratos, Instituto de Investigaciones Químicas, CSIC, Isla de la Cartuja, Seville, Spain
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