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Subedi GP, Roberts ET, Davis AR, Kremer PG, Amster IJ, Barb AW. A comprehensive assessment of selective amino acid 15N-labeling in human embryonic kidney 293 cells for NMR spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2024; 78:125-132. [PMID: 38407675 PMCID: PMC11178438 DOI: 10.1007/s10858-023-00434-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 12/31/2023] [Indexed: 02/27/2024]
Abstract
A large proportion of human proteins contain post-translational modifications that cannot be synthesized by prokaryotes. Thus, mammalian expression systems are often employed to characterize structure/function relationships using NMR spectroscopy. Here we define the selective isotope labeling of secreted, post-translationally modified proteins using human embryonic kidney (HEK)293 cells. We determined that alpha-[15N]- atoms from 10 amino acids experience minimal metabolic scrambling (C, F, H, K, M, N, R, T, W, Y). Two more interconvert to each other (G, S). Six others experience significant scrambling (A, D, E, I, L, V). We also demonstrate that tuning culture conditions suppressed V and I scrambling. These results define expectations for 15N-labeling in HEK293 cells.
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Affiliation(s)
- Ganesh P Subedi
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Elijah T Roberts
- Department of Chemistry, University of Georgia, Athens, 30602, GA, USA
| | - Alexander R Davis
- Department of Biochemistry and Molecular Biology, University of Georgia, 120 E. Green St., Athens, GA, 30602, USA
| | - Paul G Kremer
- Department of Biochemistry and Molecular Biology, University of Georgia, 120 E. Green St., Athens, GA, 30602, USA
| | - I Jonathan Amster
- Department of Chemistry, University of Georgia, Athens, 30602, GA, USA
| | - Adam W Barb
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA.
- Department of Chemistry, University of Georgia, Athens, 30602, GA, USA.
- Department of Biochemistry and Molecular Biology, University of Georgia, 120 E. Green St., Athens, GA, 30602, USA.
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA, 30602, USA.
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Lu B, Liao SM, Liang SJ, Peng LX, Li JX, Liu XH, Huang RB, Zhou GP. The Bifunctional Effects of Lactoferrin (LFcinB11) in Inhibiting Neural Cell Adhesive Molecule (NCAM) Polysialylation and the Release of Neutrophil Extracellular Traps (NETs). Int J Mol Sci 2024; 25:4641. [PMID: 38731861 PMCID: PMC11083048 DOI: 10.3390/ijms25094641] [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: 03/13/2024] [Revised: 04/17/2024] [Accepted: 04/19/2024] [Indexed: 05/13/2024] Open
Abstract
The expression of polysialic acid (polySia) on the neuronal cell adhesion molecule (NCAM) is called NCAM-polysialylation, which is strongly related to the migration and invasion of tumor cells and aggressive clinical status. Thus, it is important to select a proper drug to block tumor cell migration during clinical treatment. In this study, we proposed that lactoferrin (LFcinB11) may be a better candidate for inhibiting NCAM polysialylation when compared with CMP and low-molecular-weight heparin (LMWH), which were determined based on our NMR studies. Furthermore, neutrophil extracellular traps (NETs) represent the most dramatic stage in the cell death process, and the release of NETs is related to the pathogenesis of autoimmune and inflammatory disorders, with proposed involvement in glomerulonephritis, chronic lung disease, sepsis, and vascular disorders. In this study, the molecular mechanisms involved in the inhibition of NET release using LFcinB11 as an inhibitor were also determined. Based on these results, LFcinB11 is proposed as being a bifunctional inhibitor for inhibiting both NCAM polysialylation and the release of NETs.
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Affiliation(s)
- Bo Lu
- National Key Laboratory of Non-Food Biomass Energy Technology, National Engineering Research Center for Non-Food Biorefinery, Institute of Biological Science and Technology, Guangxi Academy of Sciences, 98 Daling Road, Nanning 530007, China; (B.L.); (S.-M.L.); (S.-J.L.); (L.-X.P.); (J.-X.L.)
| | - Si-Ming Liao
- National Key Laboratory of Non-Food Biomass Energy Technology, National Engineering Research Center for Non-Food Biorefinery, Institute of Biological Science and Technology, Guangxi Academy of Sciences, 98 Daling Road, Nanning 530007, China; (B.L.); (S.-M.L.); (S.-J.L.); (L.-X.P.); (J.-X.L.)
| | - Shi-Jie Liang
- National Key Laboratory of Non-Food Biomass Energy Technology, National Engineering Research Center for Non-Food Biorefinery, Institute of Biological Science and Technology, Guangxi Academy of Sciences, 98 Daling Road, Nanning 530007, China; (B.L.); (S.-M.L.); (S.-J.L.); (L.-X.P.); (J.-X.L.)
| | - Li-Xin Peng
- National Key Laboratory of Non-Food Biomass Energy Technology, National Engineering Research Center for Non-Food Biorefinery, Institute of Biological Science and Technology, Guangxi Academy of Sciences, 98 Daling Road, Nanning 530007, China; (B.L.); (S.-M.L.); (S.-J.L.); (L.-X.P.); (J.-X.L.)
| | - Jian-Xiu Li
- National Key Laboratory of Non-Food Biomass Energy Technology, National Engineering Research Center for Non-Food Biorefinery, Institute of Biological Science and Technology, Guangxi Academy of Sciences, 98 Daling Road, Nanning 530007, China; (B.L.); (S.-M.L.); (S.-J.L.); (L.-X.P.); (J.-X.L.)
| | - Xue-Hui Liu
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China;
| | - Ri-Bo Huang
- National Key Laboratory of Non-Food Biomass Energy Technology, National Engineering Research Center for Non-Food Biorefinery, Institute of Biological Science and Technology, Guangxi Academy of Sciences, 98 Daling Road, Nanning 530007, China; (B.L.); (S.-M.L.); (S.-J.L.); (L.-X.P.); (J.-X.L.)
- Rocky Mount Life Sciences Institute, Rocky Mount, NC 27804, USA
| | - Guo-Ping Zhou
- National Key Laboratory of Non-Food Biomass Energy Technology, National Engineering Research Center for Non-Food Biorefinery, Institute of Biological Science and Technology, Guangxi Academy of Sciences, 98 Daling Road, Nanning 530007, China; (B.L.); (S.-M.L.); (S.-J.L.); (L.-X.P.); (J.-X.L.)
- Rocky Mount Life Sciences Institute, Rocky Mount, NC 27804, USA
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Williams RV, Rogals MJ, Eletsky A, Huang C, Morris LC, Moremen KW, Prestegard JH. AssignSLP_GUI, a software tool exploiting AI for NMR resonance assignment of sparsely labeled proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2022; 345:107336. [PMID: 36442299 PMCID: PMC9742323 DOI: 10.1016/j.jmr.2022.107336] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 11/12/2022] [Accepted: 11/15/2022] [Indexed: 05/06/2023]
Abstract
Not all proteins are amenable to uniform isotopic labeling with 13C and 15N, something needed for the widely used, and largely deductive, triple resonance assignment process. Among them are proteins expressed in mammalian cell culture where native glycosylation can be maintained, and proper formation of disulfide bonds facilitated. Uniform labeling in mammalian cells is prohibitively expensive, but sparse labeling with one or a few isotopically enriched amino acid types is an option for these proteins. However, assignment then relies on accessing the best match between a variety of measured NMR parameters and predictions based on 3D structure, often from X-ray crystallography. Finding this match is a challenging process that has benefitted from many computational tools, including trained neural nets for chemical shift prediction, genetic algorithms for searches through a myriad of assignment possibilities, and now AI-based prediction of high-quality structures for protein targets. AssignSLP_GUI, a new version of a software package for assignment of resonances from sparsely-labeled proteins, uses many of these tools. These tools and new additions to the package are highlighted in an application to a sparsely-labeled domain from a glycoprotein, CEACAM1.
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Affiliation(s)
- Robert V Williams
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Monique J Rogals
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Alexander Eletsky
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Chin Huang
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Laura C Morris
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Kelley W Moremen
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - James H Prestegard
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA.
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NMR analysis suggests the terminal domains of Robo1 remain extended but are rigidified in the presence of heparan sulfate. Sci Rep 2022; 12:14769. [PMID: 36042257 PMCID: PMC9427851 DOI: 10.1038/s41598-022-18769-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/18/2022] [Indexed: 11/19/2022] Open
Abstract
Human roundabout 1 (hRobo1) is an extracellular receptor glycoprotein that plays important roles in angiogenesis, organ development, and tumor progression. Interaction between hRobo1 and heparan sulfate (HS) has been shown to be essential for its biological activity. To better understand the effect of HS binding we engineered a lanthanide-binding peptide sequence (Loop) into the Ig2 domain of hRobo1. Native mass spectrometry was used to verify that loop introduction did not inhibit HS binding or conformational changes previously suggested by gas phase ion mobility measurements. NMR experiments measuring long-range pseudocontact shifts were then performed on 13C-methyl labeled hRobo1-Ig1-2-Loop in HS-bound and unbound forms. The magnitude of most PCSs for methyl groups in the Ig1 domain increase in the bound state confirming a change in the distribution of interdomain geometries. A grid search over Ig1 orientations to optimize the fit of data to a single conformer for both forms produced two similar structures, both of which differ from existing X-ray crystal structures and structures inferred from gas-phase ion mobility measurements. The structures and degree of fit suggest that the hRobo1-Ig1-2 structure changes slightly and becomes more rigid on HS binding. This may have implications for Robo-Slit signaling.
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Prestegard JH. A perspective on the PDB's impact on the field of glycobiology. J Biol Chem 2021; 296:100556. [PMID: 33744289 PMCID: PMC8058564 DOI: 10.1016/j.jbc.2021.100556] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 03/07/2021] [Accepted: 03/16/2021] [Indexed: 12/12/2022] Open
Abstract
Structures deposited in the Protein Data Bank (PDB) facilitate our understanding of many biological processes including those that fall under the general category of glycobiology. However, structure-based studies of how glycans affect protein structure, how they are synthesized, and how they regulate other biological processes remain challenging. Despite the abundant presence of glycans on proteins and the dense layers of glycans that surround most of our cells, structures containing glycans are underrepresented in the PDB. There are sound reasons for this, including difficulties in producing proteins with well-defined glycosylation and the tendency of mobile and heterogeneous glycans to inhibit crystallization. Nevertheless, the structures we do find in the PDB, even some of the earliest deposited structures, have had an impact on our understanding of function. I highlight a few examples in this review and point to some promises for the future. Promises include new structures from methodologies, such as cryo-EM, that are less affected by the presence of glycans and experiment-aided computational methods that build on existing structures to provide insight into the many ways glycans affect biological function.
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Affiliation(s)
- James H Prestegard
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA.
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Kuprov I, Morris LC, Glushka JN, Prestegard JH. Using molecular dynamics trajectories to predict nuclear spin relaxation behaviour in large spin systems. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2021; 323:106891. [PMID: 33445107 PMCID: PMC7873838 DOI: 10.1016/j.jmr.2020.106891] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 12/07/2020] [Accepted: 12/08/2020] [Indexed: 05/09/2023]
Abstract
Molecular dynamics (MD) trajectories provide useful insights into molecular structure and dynamics. However, questions persist about the quantitative accuracy of those insights. Experimental NMR spin relaxation rates can be used as tests, but only if relaxation superoperators can be efficiently computed from MD trajectories - no mean feat for the quantum Liouville space formalism where matrix dimensions quadruple with each added spin 1/2. Here we report a module for the Spinach software framework that computes Bloch-Redfield-Wangsness relaxation superoperators (including non-secular terms and cross-correlations) from MD trajectories. Predicted initial slopes of nuclear Overhauser effects for sucrose trajectories using advanced water models and a force field optimised for glycans are within 25% of experimental values.
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Affiliation(s)
- Ilya Kuprov
- School of Chemistry, University of Southampton, Southampton, UK
| | - Laura C Morris
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, United States
| | - John N Glushka
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, United States
| | - James H Prestegard
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, United States.
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Unione L, Ardá A, Jiménez-Barbero J, Millet O. NMR of glycoproteins: profiling, structure, conformation and interactions. Curr Opin Struct Biol 2020; 68:9-17. [PMID: 33129067 DOI: 10.1016/j.sbi.2020.09.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 09/15/2020] [Accepted: 09/17/2020] [Indexed: 02/07/2023]
Abstract
In glycoproteins, carbohydrates are responsible for the selective interaction and tight regulation of cellular processes, constituting the main information transducer interface in protein-glycoprotein interactions. Increasing experimental and computational evidence suggest that such interactions often induce allosteric changes in the host protein, underlining the importance of studying intact glycoproteins. Technical issues have precluded such studies for years but, nowadays, a promising era is emerging where NMR spectroscopy, among other techniques, allows the characterization of the composition, structure and segmental dynamics of glycoproteins. In this review, we discuss such advances and highlight some selected examples. This novel technology unravels multiple new functional mechanisms, subtly hidden within the sugar code.
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Affiliation(s)
- Luca Unione
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, and Bijvoet Center for Biomolecular Research, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Ana Ardá
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Basque Research and Technology Alliance, BRTA, Bizkaia Technology Park, Building 800, 48162 Derio, Bizkaia, Spain
| | - Jesús Jiménez-Barbero
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Basque Research and Technology Alliance, BRTA, Bizkaia Technology Park, Building 800, 48162 Derio, Bizkaia, Spain; Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Bizkaia, Spain
| | - Oscar Millet
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Basque Research and Technology Alliance, BRTA, Bizkaia Technology Park, Building 800, 48162 Derio, Bizkaia, Spain.
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Kooijman L, Ansorge P, Schuster M, Baumann C, Löhr F, Jurt S, Güntert P, Zerbe O. Backbone and methyl assignment of bacteriorhodopsin incorporated into nanodiscs. JOURNAL OF BIOMOLECULAR NMR 2020; 74:45-60. [PMID: 31754899 PMCID: PMC7015963 DOI: 10.1007/s10858-019-00289-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 11/11/2019] [Indexed: 05/21/2023]
Abstract
Resonance assignments are challenging for membrane proteins due to the size of the lipid/detergent-protein complex and the presence of line-broadening from conformational exchange. As a consequence, many correlations are missing in the triple-resonance NMR experiments typically used for assignments. Herein, we present an approach in which correlations from these solution-state NMR experiments are supplemented by data from 13C unlabeling, single-amino acid type labeling, 4D NOESY data and proximity of moieties to lipids or water in combination with a structure of the protein. These additional data are used to edit the expected peaklists for the automated assignment protocol FLYA, a module of the program package CYANA. We demonstrate application of the protocol to the 262-residue proton pump from archaeal bacteriorhodopsin (bR) in lipid nanodiscs. The lipid-protein assembly is characterized by an overall correlation time of 44 ns. The protocol yielded assignments for 62% of all backbone (H, N, Cα, Cβ, C') resonances of bR, corresponding to 74% of all observed backbone spin systems, and 60% of the Ala, Met, Ile (δ1), Leu and Val methyl groups, thus enabling to assign a large fraction of the protein without mutagenesis data. Most missing resonances stem from the extracellular half, likely due intermediate exchange line-broadening. Further analysis revealed that missing information of the amino acid type of the preceding residue is the largest problem, and that 4D NOESY experiments are particularly helpful to compensate for that information loss.
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Affiliation(s)
- Laurens Kooijman
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Philipp Ansorge
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Matthias Schuster
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Christian Baumann
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Frank Löhr
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt am Main, Germany
| | - Simon Jurt
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Peter Güntert
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt am Main, Germany
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093, Zurich, Switzerland
- Department of Chemistry, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo, 192-0397, Japan
| | - Oliver Zerbe
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
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Gimeno A, Valverde P, Ardá A, Jiménez-Barbero J. Glycan structures and their interactions with proteins. A NMR view. Curr Opin Struct Biol 2019; 62:22-30. [PMID: 31835069 PMCID: PMC7322516 DOI: 10.1016/j.sbi.2019.11.004] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 11/05/2019] [Accepted: 11/07/2019] [Indexed: 12/28/2022]
Abstract
Carbohydrate molecules are essential actors in key biological events, being involved as recognition points for cell-cell and cell-matrix interactions related to health and disease. Despite outstanding advances in cryoEM, X-ray crystallography and NMR still remain the most employed techniques to unravel their conformational features and to describe the structural details of their interactions with biomolecular receptors. Given the intrinsic flexibility of saccharides, NMR methods are of paramount importance to deduce the extent of motion around their glycosidic linkages and to explore their receptor-bound conformations. We herein present our particular view on the latest advances in NMR methodologies that are permitting to magnify their applications for deducing glycan conformation and dynamics and understanding the recognition events in which there are involved.
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Affiliation(s)
- Ana Gimeno
- CIC bioGUNE, Bizkaia Technology Park, Building 800, 48162 Derio, Bizkaia, Spain
| | - Pablo Valverde
- CIC bioGUNE, Bizkaia Technology Park, Building 800, 48162 Derio, Bizkaia, Spain
| | - Ana Ardá
- CIC bioGUNE, Bizkaia Technology Park, Building 800, 48162 Derio, Bizkaia, Spain
| | - Jesús Jiménez-Barbero
- CIC bioGUNE, Bizkaia Technology Park, Building 800, 48162 Derio, Bizkaia, Spain; Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Bizkaia, Spain; Department of Organic Chemistry II, University of the Basque Country, UPV/EHU, 48940 Leioa, Bizkaia, Spain
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