1
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Prestegard JH. A consensus structural motif for the capsular polysaccharide of Cryptococcus Neoformans by NMR/MD. Proc Natl Acad Sci U S A 2024; 121:e2322413121. [PMID: 38335259 PMCID: PMC10873558 DOI: 10.1073/pnas.2322413121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2024] Open
Affiliation(s)
- James H. Prestegard
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA30601
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2
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Abdollahi H, Prestegard JH, Valafar H. Computational modeling multiple conformational states of proteins with residual dipolar coupling data. Curr Opin Struct Biol 2023; 82:102655. [PMID: 37454402 DOI: 10.1016/j.sbi.2023.102655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 06/06/2023] [Accepted: 06/20/2023] [Indexed: 07/18/2023]
Abstract
Solution nuclear magnetic resonance spectroscopy provides unique opportunities to study the structure and dynamics of biomolecules in aqueous environments. While spin relaxation methods are well recognized for their ability to probe timescales of motion, residual dipolar couplings (RDCs) provide access to amplitudes and directions of motion, characteristics that are important to the function of these molecules. Although observed in the 1960s, the acquisition and computational analysis of RDCs has gained significant momentum in recent years, and particularly applications to motion in proteins have become more numerous. This trend may well continue as RDCs can easily leverage structures produced by new computational methods (e.g., AlphaFold) to produce functional descriptions. In this report, we provide examples and a summary of the ways that RDCs have been used to confirm the existence of internal dynamics, characterize the type of dynamics, and recover atomic-scale structural ensembles that define the full range of conformational sampling.
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Affiliation(s)
- Hamed Abdollahi
- Department of Computer Science and Engineering, University of South Carolina, 29201, Columbia, SC, USA.
| | - James H Prestegard
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA.
| | - Homayoun Valafar
- Department of Computer Science and Engineering, University of South Carolina, 29201, Columbia, SC, USA.
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3
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Li EH, Spaman LE, Tejero R, Janet Huang Y, Ramelot TA, Fraga KJ, Prestegard JH, Kennedy MA, Montelione GT. Blind assessment of monomeric AlphaFold2 protein structure models with experimental NMR data. J Magn Reson 2023; 352:107481. [PMID: 37257257 PMCID: PMC10659763 DOI: 10.1016/j.jmr.2023.107481] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 05/08/2023] [Accepted: 05/15/2023] [Indexed: 06/02/2023]
Abstract
Recent advances in molecular modeling of protein structures are changing the field of structural biology. AlphaFold-2 (AF2), an AI system developed by DeepMind, Inc., utilizes attention-based deep learning to predict models of protein structures with high accuracy relative to structures determined by X-ray crystallography and cryo-electron microscopy (cryoEM). Comparing AF2 models to structures determined using solution NMR data, both high similarities and distinct differences have been observed. Since AF2 was trained on X-ray crystal and cryoEM structures, we assessed how accurately AF2 can model small, monomeric, solution protein NMR structures which (i) were not used in the AF2 training data set, and (ii) did not have homologous structures in the Protein Data Bank at the time of AF2 training. We identified nine open-source protein NMR data sets for such "blind" targets, including chemical shift, raw NMR FID data, NOESY peak lists, and (for 1 case) 15N-1H residual dipolar coupling data. For these nine small (70-108 residues) monomeric proteins, we generated AF2 prediction models and assessed how well these models fit to these experimental NMR data, using several well-established NMR structure validation tools. In most of these cases, the AF2 models fit the NMR data nearly as well, or sometimes better than, the corresponding NMR structure models previously deposited in the Protein Data Bank. These results provide benchmark NMR data for assessing new NMR data analysis and protein structure prediction methods. They also document the potential for using AF2 as a guiding tool in protein NMR data analysis, and more generally for hypothesis generation in structural biology research.
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Affiliation(s)
- Ethan H Li
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Laura E Spaman
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.
| | - Roberto Tejero
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.
| | - Yuanpeng Janet Huang
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.
| | - Theresa A Ramelot
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.
| | - Keith J Fraga
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.
| | - James H Prestegard
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA.
| | - Michael A Kennedy
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA.
| | - Gaetano T Montelione
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.
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4
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Li EH, Spaman L, Tejero R, Huang YJ, Ramelot TA, Fraga KJ, Prestegard JH, Kennedy MA, Montelione GT. Blind Assessment of Monomeric AlphaFold2 Protein Structure Models with Experimental NMR Data. bioRxiv 2023:2023.01.22.525096. [PMID: 36712039 PMCID: PMC9882346 DOI: 10.1101/2023.01.22.525096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Recent advances in molecular modeling of protein structures are changing the field of structural biology. AlphaFold-2 (AF2), an AI system developed by DeepMind, Inc., utilizes attention-based deep learning to predict models of protein structures with high accuracy relative to structures determined by X-ray crystallography and cryo-electron microscopy (cryoEM). Comparing AF2 models to structures determined using solution NMR data, both high similarities and distinct differences have been observed. Since AF2 was trained on X-ray crystal and cryoEM structures, we assessed how accurately AF2 can model small, monomeric, solution protein NMR structures which (i) were not used in the AF2 training data set, and (ii) did not have homologous structures in the Protein Data Bank at the time of AF2 training. We identified nine open source protein NMR data sets for such "blind" targets, including chemical shift, raw NMR FID data, NOESY peak lists, and (for 1 case) 15 N- 1 H residual dipolar coupling data. For these nine small (70 - 108 residues) monomeric proteins, we generated AF2 prediction models and assessed how well these models fit to these experimental NMR data, using several well-established NMR structure validation tools. In most of these cases, the AF2 models fit the NMR data nearly as well, or sometimes better than, the corresponding NMR structure models previously deposited in the Protein Data Bank. These results provide benchmark NMR data for assessing new NMR data analysis and protein structure prediction methods. They also document the potential for using AF2 as a guiding tool in protein NMR data analysis, and more generally for hypothesis generation in structural biology research. Highlights AF2 models assessed against NMR data for 9 monomeric proteins not used in training.AF2 models fit NMR data almost as well as the experimentally-determined structures. RPF-DP, PSVS , and PDBStat software provide structure quality and RDC assessment. RPF-DP analysis using AF2 models suggests multiple conformational states.
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Affiliation(s)
- Ethan H. Li
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180 USA
| | - Laura Spaman
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180 USA
| | - Roberto Tejero
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180 USA
| | - Yuanpeng Janet Huang
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180 USA
| | - Theresa A. Ramelot
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180 USA
| | - Keith J. Fraga
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180 USA
| | - James H. Prestegard
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602 USA
| | - Michael A. Kennedy
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056 USA
| | - Gaetano T. Montelione
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180 USA
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5
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Abstract
Glycans attached to glycoproteins can contribute to stability, mediate interactions with other proteins, and initiate signal transduction. Glycan conformation, which is critical to these processes, is highly variable and often depicted as sampling a multitude of conformers. These conformers can be generated by molecular dynamics simulations, and more inclusively by accelerated molecular dynamics, as well as other extended sampling methods. However, experimental assessments of the contribution that various conformers make to a native ensemble are rare. Here, we use long-range pseudo-contact shifts (PCSs) of NMR resonances from an isotopically labeled glycoprotein to identify preferred conformations of its glycans. The N-terminal domain from human Carcinoembryonic Antigen Cell Adhesion Molecule 1, hCEACAM1-Ig1, was used as the model glycoprotein in this study. It has been engineered to include a lanthanide-ion-binding loop that generates PCSs, as well as a homogeneous set of three 13C-labeled N-glycans. Analysis of the PCSs indicates that preferred glycan conformers have extensive contacts with the protein surface. Factors leading to this preference appear to include interactions between N-acetyl methyls of GlcNAc residues and hydrophobic surface pockets on the protein surface.
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6
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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. J Magn Reson 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] [What about the content of this article? (0)] [Affiliation(s)] [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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7
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Berardinelli SJ, Eletsky A, Valero-González J, Ito A, Manjunath R, Hurtado-Guerrero R, Prestegard JH, Woods RJ, Haltiwanger RS. O-fucosylation stabilizes the TSR3 motif in thrombospondin-1 by interacting with nearby amino acids and protecting a disulfide bond. J Biol Chem 2022; 298:102047. [PMID: 35597280 PMCID: PMC9198472 DOI: 10.1016/j.jbc.2022.102047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/14/2022] [Accepted: 05/16/2022] [Indexed: 11/15/2022] Open
Abstract
Thrombospondin type-1 repeats (TSRs) are small protein motifs containing six conserved cysteines forming three disulfide bonds that can be modified with an O-linked fucose. Protein O-fucosyltransferase 2 (POFUT2) catalyzes the addition of O-fucose to TSRs containing the appropriate consensus sequence, and the O-fucose modification can be elongated to a Glucose-Fucose disaccharide with the addition of glucose by β3-glucosyltransferase (B3GLCT). Elimination of Pofut2 in mice results in embryonic lethality in mice, highlighting the biological significance of O-fucose modification on TSRs. Knockout of POFUT2 in HEK293T cells has been shown to cause complete or partial loss of secretion of many proteins containing O-fucosylated TSRs. In addition, POFUT2 is localized to the endoplasmic reticulum (ER) and only modifies folded TSRs, stabilizing their structures. These observations suggest that POFUT2 is involved in an ER quality control mechanism for TSR folding and that B3GLCT also participates in quality control by providing additional stabilization to TSRs. However, the mechanisms by which addition of these sugars result in stabilization are poorly understood. Here, we conducted molecular dynamics (MD) simulations and provide crystallographic and NMR evidence that the Glucose-Fucose disaccharide interacts with specific amino acids in the TSR3 domain in thrombospondin-1 that are within proximity to the O-fucosylation modification site resulting in protection of a nearby disulfide bond. We also show that mutation of these amino acids reduces the stabilizing effect of the sugars in vitro. These data provide mechanistic details regarding the importance of O-fucosylation and how it participates in quality control mechanisms inside the ER.
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Affiliation(s)
- Steven J Berardinelli
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Resource Center, University of Georgia, Athens, Georgia, USA
| | - Alexander Eletsky
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Resource Center, University of Georgia, Athens, Georgia, USA
| | - Jessika Valero-González
- Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Zaragoza, Spain
| | - Atsuko Ito
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Resource Center, University of Georgia, Athens, Georgia, USA
| | - Rajashri Manjunath
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Resource Center, University of Georgia, Athens, Georgia, USA
| | - Ramon Hurtado-Guerrero
- Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Zaragoza, Spain; Fundación Agencia Aragonesa para la Investigación y Desarrollo (ARAID), Zaragoza, Spain; Department of Cellular and Molecular Medicine, Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, Denmark
| | - James H Prestegard
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Resource Center, University of Georgia, Athens, Georgia, USA
| | - Robert J Woods
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Resource Center, University of Georgia, Athens, Georgia, USA
| | - Robert S Haltiwanger
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Resource Center, University of Georgia, Athens, Georgia, USA.
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8
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Khaje NA, Eletsky A, Biehn SE, Mobley CK, Rogals MJ, Kim Y, Mishra SK, Doerksen RJ, Lindert S, Prestegard JH, Sharp JS. Validated determination of NRG1 Ig-like domain structure by mass spectrometry coupled with computational modeling. Commun Biol 2022; 5:452. [PMID: 35551273 PMCID: PMC9098640 DOI: 10.1038/s42003-022-03411-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 04/25/2022] [Indexed: 01/03/2023] Open
Abstract
High resolution hydroxyl radical protein footprinting (HR-HRPF) is a mass spectrometry-based method that measures the solvent exposure of multiple amino acids in a single experiment, offering constraints for experimentally informed computational modeling. HR-HRPF-based modeling has previously been used to accurately model the structure of proteins of known structure, but the technique has never been used to determine the structure of a protein of unknown structure. Here, we present the use of HR-HRPF-based modeling to determine the structure of the Ig-like domain of NRG1, a protein with no close homolog of known structure. Independent determination of the protein structure by both HR-HRPF-based modeling and heteronuclear NMR was carried out, with results compared only after both processes were complete. The HR-HRPF-based model was highly similar to the lowest energy NMR model, with a backbone RMSD of 1.6 Å. To our knowledge, this is the first use of HR-HRPF-based modeling to determine a previously uncharacterized protein structure. A mass spectrometry-based method guides computational modeling for de novo protein structure prediction.
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Affiliation(s)
- Niloofar Abolhasani Khaje
- Department of BioMolecular Sciences, University of Mississippi, University, MS, USA.,Analytical Operations Department, Gilead Sciences, Foster City, CA, USA
| | - Alexander Eletsky
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Sarah E Biehn
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, USA
| | - Charles K Mobley
- Department of BioMolecular Sciences, University of Mississippi, University, MS, USA.,Protein Discovery Department, Impossible Foods, Redwood City, CA, USA
| | - Monique J Rogals
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Yoonkyoo Kim
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Sushil K Mishra
- Department of BioMolecular Sciences, University of Mississippi, University, MS, USA.,Glycoscience Center of Research Excellence, University of Mississippi, University, MS, USA
| | - Robert J Doerksen
- Department of BioMolecular Sciences, University of Mississippi, University, MS, USA.,Glycoscience Center of Research Excellence, University of Mississippi, University, MS, USA
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, USA
| | - James H Prestegard
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Joshua S Sharp
- Department of BioMolecular Sciences, University of Mississippi, University, MS, USA. .,Glycoscience Center of Research Excellence, University of Mississippi, University, MS, USA. .,Department of Chemistry and Biochemistry, University of Mississippi, University, MS, USA.
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9
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Belcher Dufrisne M, Swope N, Kieber M, Yang JY, Han J, Li J, Moremen KW, Prestegard JH, Columbus L. Human CEACAM1 N-domain dimerization is independent from glycan modifications. Structure 2022; 30:658-670.e5. [PMID: 35219398 PMCID: PMC9081242 DOI: 10.1016/j.str.2022.02.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 11/15/2021] [Accepted: 02/01/2022] [Indexed: 12/31/2022]
Abstract
Carcinoembryonic cellular adhesion molecules (CEACAMs) serve diverse roles in cell signaling, proliferation, and survival and are made up of one or several immunoglobulin (Ig)-like ectodomains glycosylated in vivo. The physiological oligomeric state and how it contributes to protein function are central to understanding CEACAMs. Two putative dimer conformations involving different CEACAM1 N-terminal Ig-like domain (CCM1) protein faces (ABED and GFCC'C″) were identified from crystal structures. GFCC'C″ was identified as the dominant CCM1 solution dimer, but ambiguity regarding the effect of glycosylation on dimer formation calls its physiological relevance into question. We present the first crystal structure of minimally glycosylated CCM1 in the GFCC'C″ dimer conformation and characterization in solution by continuous-wave and double electron-electron resonance electron paramagnetic resonance spectroscopy. Our results suggest the GFCC'C″ dimer is dominant in solution with different levels of glycosylation, and structural conservation and co-evolved residues support that the GFCC'C″ dimer is conserved across CEACAMs.
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10
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Rogals MJ, Yang JY, Williams RV, Moremen KW, Amster IJ, Prestegard JH. Sparse isotope labeling for nuclear magnetic resonance (NMR) of glycoproteins using 13C-glucose. Glycobiology 2021; 31:425-435. [PMID: 32902634 PMCID: PMC8091466 DOI: 10.1093/glycob/cwaa071] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 07/22/2020] [Accepted: 07/24/2020] [Indexed: 01/02/2023] Open
Abstract
Preparation of samples for nuclear magnetic resonance (NMR) characterization of larger proteins requires enrichment with less abundant, NMR-active, isotopes such as 13C and 15N. This is routine for proteins that can be expressed in bacterial culture where low-cost isotopically enriched metabolic substrates can be used. However, it can be expensive for glycosylated proteins expressed in mammalian culture where more costly isotopically enriched amino acids are usually used. We describe a simple, relatively inexpensive procedure in which standard commercial media is supplemented with 13C-enriched glucose to achieve labeling of all glycans plus all alanines of the N-terminal domain of the highly glycosylated protein, CEACAM1. We demonstrate an ability to detect partially occupied N-glycan sites, sites less susceptible to processing by an endoglycosidase, and some unexpected truncation of the amino acid sequence. The labeling of both the protein (through alanines) and the glycans in a single culture requiring no additional technical expertise past standard mammalian expression requirements is anticipated to have several applications, including structural and functional screening of the many glycosylated proteins important to human health.
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Affiliation(s)
- Monique J Rogals
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd., Athens, GA 30602, USA
| | - Jeong-Yeh Yang
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd., Athens, GA 30602, USA
| | - Robert V Williams
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd., Athens, GA 30602, USA
- Department of Chemistry
| | - Kelley W Moremen
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd., Athens, GA 30602, USA
- Department of Biochemistry and Molecular Biology
| | | | - James H Prestegard
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd., Athens, GA 30602, USA
- Department of Chemistry
- Department of Biochemistry and Molecular Biology
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11
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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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12
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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. J Magn Reson 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] [What about the content of this article? (0)] [Affiliation(s)] [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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13
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Abstract
Skp1 is an adapter that links F-box proteins to cullin-1 in the Skp1/cullin-1/F-box (SCF) protein family of E3 ubiquitin ligases that targets specific proteins for polyubiquitination and subsequent protein degradation. Skp1 from the amoebozoan Dictyostelium forms a stable homodimer in vitro with a Kd of 2.5 μM as determined by sedimentation velocity studies yet is monomeric in crystal complexes with F-box proteins. To investigate the molecular basis for the difference, we determined the solution NMR structure of a doubly truncated Skp1 homodimer (Skp1ΔΔ). The solution structure of the Skp1ΔΔ dimer reveals a 2-fold symmetry with an interface that buries ∼750 Å2 of predominantly hydrophobic surface. The dimer interface overlaps with subsite 1 of the F-box interaction area, explaining why only the Skp1 monomer binds F-box proteins (FBPs). To confirm the model, Rosetta was used to predict amino acid substitutions that might disrupt the dimer interface, and the F97E substitution was chosen to potentially minimize interference with F-box interactions. A nearly full-length version of Skp1 with this substitution (Skp1ΔF97E) behaved as a stable monomer at concentrations of ≤500 μM and actively bound a model FBP, mammalian Fbs1, which suggests that the dimeric state is not required for Skp1 to carry out a basic biochemical function. Finally, Skp1ΔF97E is expected to serve as a monomer model for high-resolution NMR studies previously hindered by dimerization.
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Affiliation(s)
- Hyun W. Kim
- Dept. of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602 USA
| | - Alexander Eletsky
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602 USA
| | - Karen J. Gonzalez
- Dept. of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA 30602 USA
| | - Hanke van der Wel
- Dept. of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602 USA
| | - Eva-Maria Strauch
- Dept. of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA 30602 USA
| | - James H. Prestegard
- Dept. of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602 USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602 USA
| | - Christopher M. West
- Dept. of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602 USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602 USA
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA 30602 USA
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14
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Zhuo Y, Yang JY, Moremen KW, Prestegard JH. Correction: Glycosylation alters dimerization properties of a cell-surface signaling protein, carcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1). J Biol Chem 2020; 295:3748. [PMID: 32169858 DOI: 10.1074/jbc.aac120.013039] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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15
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Williams RV, Yang JY, Moremen KW, Amster IJ, Prestegard JH. Measurement of residual dipolar couplings in methyl groups via carbon detection. J Biomol NMR 2019; 73:191-198. [PMID: 31041649 PMCID: PMC7020099 DOI: 10.1007/s10858-019-00245-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 03/30/2019] [Indexed: 06/09/2023]
Abstract
Residual dipolar couplings (RDCs) provide both structural and dynamical information useful in the characterization of biological macromolecules. While most data come from the interaction of simple pairs of directly bonded spin-1/2 nuclei (1H-15N, 1H-13C, 1H-1H), it is possible to acquire data from interactions among the multiple spins of 13C-labeled methyl groups (1H3-13C). This is especially important because of the advantages that observation of 13C-labeled methyl groups offers in working with very large molecules. Here we consider some of the options for measurement of methyl RDCs in large and often fully protonated proteins and arrive at a pulse sequence that exploits both J-modulation and direct detection of 13C. Its utility is illustrated by application to a fully protonated two domain fragment from the mammalian glycoprotein, Robo1, 13C-methyl-labeled in all valines.
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Affiliation(s)
- Robert V Williams
- Department of Chemistry, University of Georgia, Athens, GA, USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Jeong-Yeh Yang
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Kelley W Moremen
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | | | - James H Prestegard
- Department of Chemistry, University of Georgia, Athens, GA, USA.
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA.
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA.
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16
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Prestegard JH, Moremen KW, Amster IJ, Williams RV, Eletsky A, Chalmers GR, Morris LC, Yang J, Chapla D. Structural Aspects of Glycosylated Protein–Glycan Interactions by NMR. FASEB J 2019. [DOI: 10.1096/fasebj.2019.33.1_supplement.800.4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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17
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Moure MJ, Eletsky A, Gao Q, Morris LC, Yang JY, Chapla D, Zhao Y, Zong C, Amster IJ, Moremen KW, Boons GJ, Prestegard JH. Paramagnetic Tag for Glycosylation Sites in Glycoproteins: Structural Constraints on Heparan Sulfate Binding to Robo1. ACS Chem Biol 2018; 13:2560-2567. [PMID: 30063822 PMCID: PMC6161356 DOI: 10.1021/acschembio.8b00511] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An enzyme- and click chemistry-mediated methodology for the site-specific nitroxide spin labeling of glycoproteins has been developed and applied. The procedure relies on the presence of single N-glycosylation sites that are present natively in proteins or that can be engineered into glycoproteins by mutational elimination of all but one glycosylation site. Recombinantly expressing glycoproteins in HEK293S (GnT1-) cells results in N-glycans with high-mannose structures that can be processed to leave a single GlcNAc residue. This can in turn be modified by enzymatic addition of a GalNAz residue that is subject to reaction with an alkyne-carrying TEMPO moiety using copper(I)-catalyzed click chemistry. To illustrate the procedure, we have made an application to a two-domain construct of Robo1, a protein that carries a single N-glycosylation site in its N-terminal domains. The construct has also been labeled with 15N at amide nitrogens of lysine residues to provide a set of sites that are used to derive an effective location of the paramagnetic nitroxide moiety of the TEMPO group. This, in turn, allowed measurements of paramagnetic perturbations to the spectra of a new high affinity heparan sulfate ligand. Calculation of distance constraints from these data facilitated determination of an atomic level model for the docked complex.
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Affiliation(s)
- Maria J. Moure
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
| | - Alexander Eletsky
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
| | - Qi Gao
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Laura C. Morris
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
| | - Jeong-Yeh Yang
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
| | - Digantkumar Chapla
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
| | - Yuejie Zhao
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Chengli Zong
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
| | - I. Jonathan Amster
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Kelley W. Moremen
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, United States
| | - Geert-Jan Boons
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, and Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - James H. Prestegard
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, United States
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18
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Gao Q, Yang JY, Moremen KW, Flanagan JG, Prestegard JH. Structural Characterization of a Heparan Sulfate Pentamer Interacting with LAR-Ig1-2. Biochemistry 2018; 57:2189-2199. [PMID: 29570275 DOI: 10.1021/acs.biochem.8b00241] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Leukocyte common antigen-related (LAR) protein is one of the type IIa receptor protein tyrosine phosphatases (RPTPs) that are important for signal transduction in biological processes, including axon growth and regeneration. Glycosaminoglycan chains, including heparan sulfate (HS) and chondroitin sulfate (CS), act as ligands that regulate LAR signaling. Here, we report the structural characterization of the first two immunoglobulin domains (Ig1-2) of LAR interacting with an HS pentasaccharide (GlcNS6S-GlcA-GlcNS3,6S-IdoA2S-GlcNS6S-OME, fondaparinux) using multiple solution-based NMR methods. In the course of the study, we extended an assignment strategy useful for sparsely labeled proteins expressed in mammalian cell culture supplemented with a single type of isotopically enriched amino acid ([15N]-Lys in this case) by including paramagnetic perturbations to NMR resonances. The folded two-domain structure for LAR-Ig1-2 seen in previous crystal structures has been validated in solution using residual dipolar coupling data, and a combination of chemical shift perturbation on titration of LAR-Ig1-2 with fondaparinux, saturation transfer difference (STD) spectra, and transferred nuclear Overhauser effects (trNOEs) have been employed in the docking program HADDOCK to generate models for the LAR-fondaparinux complex. These models are further analyzed by postprocessing energetic analysis to identify key binding interactions. In addition to providing insight into the ligand interaction mechanisms of type IIa RPTPs and the origin of opposing effects of CS and HS ligands, these results may assist in future design of therapeutic compounds for nervous system repair.
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Affiliation(s)
- Qi Gao
- Complex Carbohydrate Research Center , University of Georgia , Athens , Georgia 30602 , United States
| | - Jeong-Yeh Yang
- Complex Carbohydrate Research Center , University of Georgia , Athens , Georgia 30602 , United States
| | - Kelley W Moremen
- Complex Carbohydrate Research Center , University of Georgia , Athens , Georgia 30602 , United States
| | - John G Flanagan
- Department of Cell Biology and Program in Neuroscience , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - James H Prestegard
- Complex Carbohydrate Research Center , University of Georgia , Athens , Georgia 30602 , United States
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19
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Xu X, Eletsky A, Sheikh MO, Prestegard JH, West CM. Glycosylation Promotes the Random Coil to Helix Transition in a Region of a Protist Skp1 Associated with F-Box Binding. Biochemistry 2017; 57:511-515. [PMID: 29251491 DOI: 10.1021/acs.biochem.7b01033] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cullin-ring-ligases mediate protein polyubiquitination, a signal for degradation in the 26S proteasome. The CRL1 class consists of Skp1/cullin-1/F-box protein/Rbx1 (SCF) complexes that cyclically associate with ubiquitin-E2 to build the polyubiquitin chain. Within the SCF complex, the 162-amino acid DdSkp1 from Dictyostelium bridges cullin-1 with an F-box protein (FBP), the specificity factor for substrate selection. The hydroxylation-dependent glycosylation of Pro143 of DdSkp1 by a pentasaccharide forms the basis of a novel O2-sensing mechanism in the social amoeba Dictyostelium and other protists. Previous evidence indicated that glycosylation promotes increased α-helical content correlating with enhanced interaction with three F-box proteins. To localize these differences, we used nuclear magnetic resonance (NMR) methods to compare nonglycosylated DdSkp1 and a glycoform with a single GlcNAc sugar (Gn-DdSkp1). We report NMR assignments of backbone 1HN, 15N, 13Cα, and 13CO nuclei as well as side-chain 13Cβ and methyl 13C/1H nuclei of Ile(δ1), Leu, and Val in both unmodified DdSkp1 and Gn-DdSkp1. The random coil index and 15N{1H} HNOE indicate that the C-terminal region, which forms a helix-loop-helix motif centered on Pro143 at the crystallographically defined binding interface with F-box domains, remains dynamic in both DdSkp1 and Gn-DdSkp1. Chemical shifts indicate that the variation of conformation in Gn-DdSkp1, relative to DdSkp1, is limited to this region and characterized by increased helical fold. Extension of the glycan chain results in further changes, also limited to this region. Thus, glycosylation may control F-box protein interactions via a local effect on DdSkp1 conformation, by a mechanism that may be general to many unicellular eukaryotes.
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Affiliation(s)
- Xianzhong Xu
- Department of Biochemistry & Molecular Biology, ‡Complex Carbohydrate Research Center, and §Center for Tropical and Emerging Global Diseases, University of Georgia , Athens, Georgia 30602, United States
| | - Alexander Eletsky
- Department of Biochemistry & Molecular Biology, ‡Complex Carbohydrate Research Center, and §Center for Tropical and Emerging Global Diseases, University of Georgia , Athens, Georgia 30602, United States
| | - M Osman Sheikh
- Department of Biochemistry & Molecular Biology, ‡Complex Carbohydrate Research Center, and §Center for Tropical and Emerging Global Diseases, University of Georgia , Athens, Georgia 30602, United States
| | - James H Prestegard
- Department of Biochemistry & Molecular Biology, ‡Complex Carbohydrate Research Center, and §Center for Tropical and Emerging Global Diseases, University of Georgia , Athens, Georgia 30602, United States
| | - Christopher M West
- Department of Biochemistry & Molecular Biology, ‡Complex Carbohydrate Research Center, and §Center for Tropical and Emerging Global Diseases, University of Georgia , Athens, Georgia 30602, United States
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20
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Sheikh MO, Thieker D, Chalmers G, Schafer CM, Ishihara M, Azadi P, Woods RJ, Glushka JN, Bendiak B, Prestegard JH, West CM. O 2 sensing-associated glycosylation exposes the F-box-combining site of the Dictyostelium Skp1 subunit in E3 ubiquitin ligases. J Biol Chem 2017; 292:18897-18915. [PMID: 28928219 PMCID: PMC5704474 DOI: 10.1074/jbc.m117.809160] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 09/12/2017] [Indexed: 11/06/2022] Open
Abstract
Skp1 is a conserved protein linking cullin-1 to F-box proteins in SCF (Skp1/Cullin-1/F-box protein) E3 ubiquitin ligases, which modify protein substrates with polyubiquitin chains that typically target them for 26S proteasome-mediated degradation. In Dictyostelium (a social amoeba), Toxoplasma gondii (the agent for human toxoplasmosis), and other protists, Skp1 is regulated by a unique pentasaccharide attached to hydroxylated Pro-143 within its C-terminal F-box-binding domain. Prolyl hydroxylation of Skp1 contributes to O2-dependent Dictyostelium development, but full glycosylation at that position is required for optimal O2 sensing. Previous studies have shown that the glycan promotes organization of the F-box-binding region in Skp1 and aids in Skp1's association with F-box proteins. Here, NMR and MS approaches were used to determine the glycan structure, and then a combination of NMR and molecular dynamics simulations were employed to characterize the impact of the glycan on the conformation and motions of the intrinsically flexible F-box-binding domain of Skp1. Molecular dynamics trajectories of glycosylated Skp1 whose calculated monosaccharide relaxation kinetics and rotational correlation times agreed with the NMR data indicated that the glycan interacts with the loop connecting two α-helices of the F-box-combining site. In these trajectories, the helices separated from one another to create a more accessible and dynamic F-box interface. These results offer an unprecedented view of how a glycan modification influences a disordered region of a full-length protein. The increased sampling of an open Skp1 conformation can explain how glycosylation enhances interactions with F-box proteins in cells.
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Affiliation(s)
- M Osman Sheikh
- From the Department of Biochemistry and Molecular Biology
- the Complex Carbohydrate Research Center, and
- the Department of Biochemistry and Molecular Biology, Oklahoma Center for Medical Glycobiology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, and
| | | | - Gordon Chalmers
- the Complex Carbohydrate Research Center, and
- the Department of Computer Science, University of Georgia, Athens, Georgia 30602
| | - Christopher M Schafer
- the Department of Biochemistry and Molecular Biology, Oklahoma Center for Medical Glycobiology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, and
| | | | | | - Robert J Woods
- From the Department of Biochemistry and Molecular Biology
- the Complex Carbohydrate Research Center, and
| | | | - Brad Bendiak
- the Department of Cell and Developmental Biology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045
| | - James H Prestegard
- From the Department of Biochemistry and Molecular Biology
- the Complex Carbohydrate Research Center, and
| | - Christopher M West
- From the Department of Biochemistry and Molecular Biology,
- the Department of Biochemistry and Molecular Biology, Oklahoma Center for Medical Glycobiology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, and
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21
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Zhuo Y, Cordeiro CD, Hekmatyar SK, Docampo R, Prestegard JH. Dynamic nuclear polarization facilitates monitoring of pyruvate metabolism in Trypanosoma brucei. J Biol Chem 2017; 292:18161-18168. [PMID: 28887303 DOI: 10.1074/jbc.m117.807495] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Indexed: 11/06/2022] Open
Abstract
Dynamic nuclear polarization provides sensitivity improvements that make NMR a viable method for following metabolic conversions in real time. There are now many in vivo applications to animal systems and even to diagnosis of human disease. However, application to microbial systems is rare. Here we demonstrate its application to the pathogenic protozoan, Trypanosoma brucei, using hyperpolarized 13C1 pyruvate as a substrate and compare the parasite metabolism with that of commonly cultured mammalian cell lines, HEK-293 and Hep-G2. Metabolic differences between insect and bloodstream forms of T. brucei were also investigated. Significant differences are noted with respect to lactate, alanine, and CO2 production. Conversion of pyruvate to CO2 in the T. brucei bloodstream form provides new support for the presence of an active pyruvate dehydrogenase in this stage.
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Affiliation(s)
- You Zhuo
- From the Complex Carbohydrate Research Center
| | - Ciro D Cordeiro
- the Center for Tropical and Emerging Global Diseases, and.,the Department of Cellular Biology, University of Georgia, Athens, Georgia 30602
| | | | - Roberto Docampo
- the Center for Tropical and Emerging Global Diseases, and.,the Department of Cellular Biology, University of Georgia, Athens, Georgia 30602
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22
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Pederson K, Chalmers GR, Gao Q, Elnatan D, Ramelot TA, Ma LC, Montelione GT, Kennedy MA, Agard DA, Prestegard JH. NMR characterization of HtpG, the E. coli Hsp90, using sparse labeling with 13C-methyl alanine. J Biomol NMR 2017; 68:225-236. [PMID: 28653216 PMCID: PMC5546222 DOI: 10.1007/s10858-017-0123-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 06/22/2017] [Indexed: 05/03/2023]
Abstract
A strategy for acquiring structural information from sparsely isotopically labeled large proteins is illustrated with an application to the E. coli heat-shock protein, HtpG (high temperature protein G), a 145 kDa dimer. It uses 13C-alanine methyl labeling in a perdeuterated background to take advantage of the sensitivity and resolution of Methyl-TROSY spectra, as well as the backbone-centered structural information from 1H-13C residual dipolar couplings (RDCs) of alanine methyl groups. In all, 40 of the 47 expected crosspeaks were resolved and 36 gave RDC data. Assignments of crosspeaks were partially achieved by transferring assignments from those made on individual domains using triple resonance methods. However, these were incomplete and in many cases the transfer was ambiguous. A genetic algorithm search for consistency between predictions based on domain structures and measurements for chemical shifts and RDCs allowed 60% of the 40 resolved crosspeaks to be assigned with confidence. Chemical shift changes of these crosspeaks on adding an ATP analog to the apo-protein are shown to be consistent with structural changes expected on comparing previous crystal structures for apo- and complex- structures. RDCs collected on the assigned alanine methyl peaks are used to generate a new solution model for the apo-protein structure.
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Affiliation(s)
- Kari Pederson
- Complex Carbohydrate Research Center, University of Georgia, Athens, USA
| | - Gordon R Chalmers
- Complex Carbohydrate Research Center, University of Georgia, Athens, USA
- Department of Computer Science, University of Georgia, Athens, USA
| | - Qi Gao
- Complex Carbohydrate Research Center, University of Georgia, Athens, USA
| | - Daniel Elnatan
- Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of California, San Francisco, USA
| | - Theresa A Ramelot
- Department of Chemistry and Biochemistry, Miami University, Oxford, USA
| | - Li-Chung Ma
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, The State University of New Jersey, Piscataway, USA
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, USA
| | - Gaetano T Montelione
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, The State University of New Jersey, Piscataway, USA
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, USA
| | - Michael A Kennedy
- Department of Chemistry and Biochemistry, Miami University, Oxford, USA
| | - David A Agard
- Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of California, San Francisco, USA
| | - James H Prestegard
- Complex Carbohydrate Research Center, University of Georgia, Athens, USA.
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23
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Abstract
Mistakes in translation of messenger RNA into protein are clearly a detriment to the recombinant production of pure proteins for biophysical study or the biopharmaceutical market. However, they may also provide insight into mechanistic details of the translation process. Mistakes often involve the substitution of an amino acid having an abundant codon for one having a rare codon, differing by substitution of a G base by an A base, as in the case of substitution of a lysine (AAA) for arginine (AGA). In these cases one expects the substitution frequency to depend on the relative abundances of the respective tRNAs, and thus, one might expect frequencies to be similar for all sites having the same rare codon. Here we demonstrate that, for the ADP-ribosylation factor from yeast expressed in E. coli, lysine for arginine substitutions frequencies are not the same at the 9 sites containing a rare arginine codon; mis-incorporation frequencies instead vary from less than 1 to 16%. We suggest that the context in which the codons occur (clustering of rare sites) may be responsible for the variation. The method employed to determine the frequency of mis-incorporation involves a novel mass spectrometric analysis of the products from the parallel expression of wild type and codon-optimized genes in 15N and 14N enriched media, respectively. The high sensitivity and low material requirements of the method make this a promising technology for the collection of data relevant to other mis-incorporations. The additional data could be of value in refining models for the ribosomal translation elongation process.
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Affiliation(s)
- Yizhou Liu
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, United States of America
| | - Joshua S. Sharp
- Department of BioMolecular Sciences, University of Mississippi, Oxford, Mississippi, United States of America
| | - Duc H-T. Do
- Department of Food Science and Technology, University of Georgia, Athens, Georgia, United States of America
| | - Richard A. Kahn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University, Frankfurt, Germany
| | - Florian Buhr
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University, Frankfurt, Germany
| | - James H. Prestegard
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, United States of America
- * E-mail:
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24
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Gao Q, Chalmers GR, Moremen KW, Prestegard JH. NMR assignments of sparsely labeled proteins using a genetic algorithm. J Biomol NMR 2017; 67:283-294. [PMID: 28289927 PMCID: PMC5434516 DOI: 10.1007/s10858-017-0101-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 02/22/2017] [Indexed: 05/16/2023]
Abstract
Sparse isotopic labeling of proteins for NMR studies using single types of amino acid (15N or 13C enriched) has several advantages. Resolution is enhanced by reducing numbers of resonances for large proteins, and isotopic labeling becomes economically feasible for glycoproteins that must be expressed in mammalian cells. However, without access to the traditional triple resonance strategies that require uniform isotopic labeling, NMR assignment of crosspeaks in heteronuclear single quantum coherence (HSQC) spectra is challenging. We present an alternative strategy which combines readily accessible NMR data with known protein domain structures. Based on the structures, chemical shifts are predicted, NOE cross-peak lists are generated, and residual dipolar couplings (RDCs) are calculated for each labeled site. Simulated data are then compared to measured values for a trial set of assignments and scored. A genetic algorithm uses the scores to search for an optimal pairing of HSQC crosspeaks with labeled sites. While none of the individual data types can give a definitive assignment for a particular site, their combination can in most cases. Four test proteins previously assigned using triple resonance methods and a sparsely labeled glycosylated protein, Robo1, previously assigned by manual analysis, are used to validate the method and develop a criterion for identifying sites assigned with high confidence.
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Affiliation(s)
- Qi Gao
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Gordon R Chalmers
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
- Department of Computer Science and 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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25
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Gao Q, Chen CY, Zong C, Wang S, Ramiah A, Prabhakar P, Morris LC, Boons GJ, Moremen KW, Prestegard JH. Structural Aspects of Heparan Sulfate Binding to Robo1-Ig1-2. ACS Chem Biol 2016; 11:3106-3113. [PMID: 27653286 PMCID: PMC5148660 DOI: 10.1021/acschembio.6b00692] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Roundabout 1, or Robo1, is a cell surface signaling molecule important in axon guidance. Its interaction with heparan sulfate (HS) and members of the Slit protein family is essential to its activity, making characterization of these interactions by structural methods, such as NMR, highly desirable. However, the fact that Robo1 is a glycosylated protein prevents employment of commonly used bacterial hosts for expression of properly glycosylated forms with the uniform 15N, 13C, and 2H labeling needed for NMR studies. Here, we apply an alternative methodology, based on labeling with a single amino acid type and high structural content NMR data, to characterize a two-domain construct of glycosylated Robo1 (Robo1-Ig1-2) interacting with a synthetic HS tetramer (IdoA-GlcNS6S-IdoA2S-GlcNS6S-(CH2)5NH2). Significant chemical shift perturbations of the crosspeak from K81 on titration with the tetramer provide initial evidence for the location of a binding site and allow determination of a 255 μM disassociation constant. The binding epitopes, bound conformation, and binding site placement of the HS tetramer have been further characterized by saturation transfer difference (STD), transferred nuclear Overhauser effect (trNOE), and paramagnetic perturbation experiments. A model of the complex has been generated using constraints derived from the various NMR experiments. Postprocessing energetic analysis of this model provides a rationale for the role each glycan residue plays in the binding event, and examination of the binding site in the context of a previous Robo-Slit structure provides a rationale for modulation of Robo-Slit interactions by HS.
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Affiliation(s)
- Qi Gao
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
| | - Cheng-Yu Chen
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
| | - Chengli Zong
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
| | - Shuo Wang
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
| | - Annapoorani Ramiah
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
| | - Pradeep Prabhakar
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
| | - Laura C. Morris
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
| | - Geert-Jan Boons
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
| | - Kelley W. Moremen
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
| | - James H. Prestegard
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
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26
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Singh A, Tessier MB, Pederson K, Wang X, Venot AP, Boons GJ, Prestegard JH, Woods RJ. Extension and validation of the GLYCAM force field parameters for modeling glycosaminoglycans. CAN J CHEM 2016; 94:927-935. [PMID: 28603292 PMCID: PMC5464424 DOI: 10.1139/cjc-2015-0606] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Glycosaminoglycans (GAGs) are an important class of carbohydrates that serve critical roles in blood clotting, tissue repair, cell migration and adhesion, and lubrication. The variable sulfation pattern and iduronate ring conformations in GAGs influence their polymeric structure and nature of interaction. This study characterizes several heparin-like GAG disaccharides and tetrasaccharides using NMR and molecular dynamics simulations to assist in the development of parameters for GAGs within the GLYCAM06 force field. The force field additions include parameters and charges for a transferable sulfate group for O- and N-sulfation, neutral (COOH) forms of iduronic and glucuronic acid, and Δ4,5-unsaturated uronate (ΔUA) residues. ΔUA residues frequently arise from the enzymatic digestion of heparin and heparin sulfate. Simulations of disaccharides containing ΔUA reveal that the presence of sulfation on this residue alters the relative populations of 1H2 and 2H1 ring conformations. Simulations of heparin tetrasaccharides containing N-sulfation in place of N-acetylation on glucosamine residues influence the ring conformations of adjacent iduronate residues.
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Affiliation(s)
- Arunima Singh
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
| | - Matthew B Tessier
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
| | - Kari Pederson
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
| | - Xiaocong Wang
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
| | - Andre P Venot
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
| | - Geert-Jan Boons
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
| | - James H Prestegard
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
| | - Robert J Woods
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
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27
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Zhuo Y, Yang JY, Moremen KW, Prestegard JH. Glycosylation Alters Dimerization Properties of a Cell-surface Signaling Protein, Carcinoembryonic Antigen-related Cell Adhesion Molecule 1 (CEACAM1). J Biol Chem 2016; 291:20085-95. [PMID: 27471271 DOI: 10.1074/jbc.m116.740050] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Indexed: 12/12/2022] Open
Abstract
Human carcinoembryonic antigen-related cell adhesion molecule 1 (C?/Au: EACAM1) is a cell-surface signaling molecule involved in cell adhesion, proliferation, and immune response. It is also implicated in cancer angiogenesis, progression, and metastasis. This diverse set of effects likely arises as a result of the numerous homophilic and heterophilic interactions that CEACAM1 can have with itself and other molecules. Its N-terminal Ig variable (IgV) domain has been suggested to be a principal player in these interactions. Previous crystal structures of the β-sandwich-like IgV domain have been produced using Escherichia coli-expressed material, which lacks native glycosylation. These have led to distinctly different proposals for dimer interfaces, one involving interactions of ABED β-strands and the other involving GFCC'C″ β-strands, with the former burying one prominent glycosylation site. These structures raise questions as to which form may exist in solution and what the effect of glycosylation may have on this form. Here, we use NMR cross-correlation measurements to examine the effect of glycosylation on CEACAM1-IgV dimerization and use residual dipolar coupling (RDC) measurements to characterize the solution structure of the non-glycosylated form. Our findings demonstrate that even addition of a single N-linked GlcNAc at potential glycosylation sites inhibits dimer formation. Surprisingly, RDC data collected on E. coli expressed material in solution indicate that a dimer using the non-glycosylated GFCC'C″ interface is preferred even in the absence of glycosylation. The results open new questions about what other factors may facilitate dimerization of CEACAM1 in vivo, and what roles glycosylation may play in heterophylic interactions.
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Affiliation(s)
- You Zhuo
- From the Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
| | - Jeong-Yeh Yang
- From the Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
| | - Kelley W Moremen
- From the Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
| | - James H Prestegard
- From the Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
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28
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Chalmers G, Glushka JN, Foley BL, Woods RJ, Prestegard JH. Direct NOE simulation from long MD trajectories. J Magn Reson 2016; 265:1-9. [PMID: 26826977 PMCID: PMC4818662 DOI: 10.1016/j.jmr.2016.01.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 01/10/2016] [Accepted: 01/12/2016] [Indexed: 05/08/2023]
Abstract
A software package, MD2NOE, is presented which calculates Nuclear Overhauser Effect (NOE) build-up curves directly from molecular dynamics (MD) trajectories. It differs from traditional approaches in that it calculates correlation functions directly from the trajectory instead of extracting inverse sixth power distance terms as an intermediate step in calculating NOEs. This is particularly important for molecules that sample conformational states on a timescale similar to molecular reorientation. The package is tested on sucrose and results are shown to differ in small but significant ways from those calculated using an inverse sixth power assumption. Results are also compared to experiment and found to be in reasonable agreement despite an expected underestimation of water viscosity by the water model selected.
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Affiliation(s)
- G Chalmers
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, United States
| | - J N Glushka
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, United States
| | - B L Foley
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, United States
| | - R J Woods
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, United States
| | - J H Prestegard
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, United States.
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29
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Abstract
The growing importance of biologics and biosimilars as therapeutic and diagnostic agents is giving rise to new demands for analytical methodology that can quickly and accurately assess the chemical and physical state of protein-based products. A particular challenge exists in physical characterization where the proper fold and extent of disorder of a protein is a major concern. The ability of NMR to reflect structural and dynamic properties of proteins is well recognized, but sensitivity limitations and high levels of interference from excipients in typical biologic formulations have prevented widespread applications to quality assessment. Here we demonstrate applicability of a simple one-dimensional proton NMR method that exploits enhanced spin diffusion among protons in well-structured areas of a protein. We show that it is possible to reduce excipient signals and allow focus on structural characteristics of the protein. Additional decomposition of the resulting spectra based on rotating frame spin relaxation allows separate examination of components from aggregates and disordered regions. Application to a comparison of two different monoclonal antibodies and to detection of partial pH denaturation of a monoclonal antibody illustrates the procedure.
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Affiliation(s)
- Joshua Franks
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602
| | - John N. Glushka
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602
| | - Michael T. Jones
- Analytical Research and Development, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc, St. Louis MO
| | - David H. Live
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602
| | - Qin Zou
- Analytical Research and Development, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc, St. Louis MO
| | - James H. Prestegard
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602
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30
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Park Y, Jowitt TA, Day AJ, Prestegard JH. Nuclear Magnetic Resonance Insight into the Multiple Glycosaminoglycan Binding Modes of the Link Module from Human TSG-6. Biochemistry 2016; 55:262-76. [PMID: 26685054 PMCID: PMC5073374 DOI: 10.1021/acs.biochem.5b01148] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Tumor necrosis factor-stimulated gene-6 (TSG-6) is a hyaluronan (HA)-binding protein that is essential for stabilizing and remodeling the extracellular matrix (ECM) during ovulation and inflammatory disease processes such as arthritis. The Link module, one of the domains of TSG-6, is responsible for binding hyaluronan and other glycosaminoglycans found in the ECM. In this study, we used a well-defined chondroitin sulfate (CS) hexasaccharide (ΔC444S) to determine the structure of the Link module, in solution, in its chondroitin sulfate-bound state. A variety of nuclear magnetic resonance techniques were employed, including chemical shift perturbation, residual dipolar couplings (RDCs), nuclear Overhauser effects, spin relaxation measurements, and paramagnetic relaxation enhancements from a spin-labeled analogue of ΔC444S. The binding site for ΔC444S on the Link module overlapped with that of HA. Surprisingly, ΔC444S binding induced dimerization of the Link module (as confirmed by analytical ultracentrifugation), and a second weak binding site that partially overlapped with a previously identified heparin site was detected. A dimer model was generated using chemical shift perturbations and RDCs as restraints in the docking program HADDOCK. We postulate that the molecular cross-linking enhanced by the multiple binding modes of the Link module might be critical for remodeling the ECM during inflammation/ovulation and might contribute to other functions of TSG-6.
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Affiliation(s)
- Younghee Park
- Complex Carbohydrate Research Center, 315 Riverbend Road, University of Georgia, Athens, GA 30602, USA
| | - Thomas A. Jowitt
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Anthony J. Day
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - James H. Prestegard
- Complex Carbohydrate Research Center, 315 Riverbend Road, University of Georgia, Athens, GA 30602, USA
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Everett JK, Tejero R, Murthy SBK, Acton TB, Aramini JM, Baran MC, Benach J, Cort JR, Eletsky A, Forouhar F, Guan R, Kuzin AP, Lee HW, Liu G, Mani R, Mao B, Mills JL, Montelione AF, Pederson K, Powers R, Ramelot T, Rossi P, Seetharaman J, Snyder D, Swapna GVT, Vorobiev SM, Wu Y, Xiao R, Yang Y, Arrowsmith CH, Hunt JF, Kennedy MA, Prestegard JH, Szyperski T, Tong L, Montelione GT. A community resource of experimental data for NMR / X-ray crystal structure pairs. Protein Sci 2015; 25:30-45. [PMID: 26293815 DOI: 10.1002/pro.2774] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 08/17/2015] [Indexed: 12/11/2022]
Abstract
We have developed an online NMR / X-ray Structure Pair Data Repository. The NIGMS Protein Structure Initiative (PSI) has provided many valuable reagents, 3D structures, and technologies for structural biology. The Northeast Structural Genomics Consortium was one of several PSI centers. NESG used both X-ray crystallography and NMR spectroscopy for protein structure determination. A key goal of the PSI was to provide experimental structures for at least one representative of each of hundreds of targeted protein domain families. In some cases, structures for identical (or nearly identical) constructs were determined by both NMR and X-ray crystallography. NMR spectroscopy and X-ray diffraction data for 41 of these "NMR / X-ray" structure pairs determined using conventional triple-resonance NMR methods with extensive sidechain resonance assignments have been organized in an online NMR / X-ray Structure Pair Data Repository. In addition, several NMR data sets for perdeuterated, methyl-protonated protein samples are included in this repository. As an example of the utility of this repository, these data were used to revisit questions about the precision and accuracy of protein NMR structures first outlined by Levy and coworkers several years ago (Andrec et al., Proteins 2007;69:449-465). These results demonstrate that the agreement between NMR and X-ray crystal structures is improved using modern methods of protein NMR spectroscopy. The NMR / X-ray Structure Pair Data Repository will provide a valuable resource for new computational NMR methods development.
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Affiliation(s)
- John K Everett
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, and Northeast Structural Genomics Consortium, Rutgers, the State University of New Jersey, Piscataway, New Jersey, 08854, USA
| | - Roberto Tejero
- Departamento De Química Física, Universidad De Valencia, Valencia, Spain
| | - Sarath B K Murthy
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, and Northeast Structural Genomics Consortium, Rutgers, the State University of New Jersey, Piscataway, New Jersey, 08854, USA
| | - Thomas B Acton
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, and Northeast Structural Genomics Consortium, Rutgers, the State University of New Jersey, Piscataway, New Jersey, 08854, USA
| | - James M Aramini
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, and Northeast Structural Genomics Consortium, Rutgers, the State University of New Jersey, Piscataway, New Jersey, 08854, USA
| | - Michael C Baran
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, and Northeast Structural Genomics Consortium, Rutgers, the State University of New Jersey, Piscataway, New Jersey, 08854, USA
| | - Jordi Benach
- Department of Biological Sciences and Northeast Structural Genomics Consortium, Columbia University, New York, NY, 10027, USA
| | - John R Cort
- Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, 99354, USA
| | - Alexander Eletsky
- Department of Chemistry, The State University of New York at Buffalo, and Northeast Structural Genomics Consortium, Buffalo, New York, 14260, USA
| | - Farhad Forouhar
- Department of Biological Sciences and Northeast Structural Genomics Consortium, Columbia University, New York, NY, 10027, USA
| | - Rongjin Guan
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, and Northeast Structural Genomics Consortium, Rutgers, the State University of New Jersey, Piscataway, New Jersey, 08854, USA
| | - Alexandre P Kuzin
- Department of Biological Sciences and Northeast Structural Genomics Consortium, Columbia University, New York, NY, 10027, USA
| | - Hsiau-Wei Lee
- Complex Carbohydrate Research Center and Northeast Structural Genomics Consortium, University of Georgia, Athens, Georgia, 30602, USA
| | - Gaohua Liu
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, and Northeast Structural Genomics Consortium, Rutgers, the State University of New Jersey, Piscataway, New Jersey, 08854, USA
| | - Rajeswari Mani
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, and Northeast Structural Genomics Consortium, Rutgers, the State University of New Jersey, Piscataway, New Jersey, 08854, USA
| | - Binchen Mao
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, and Northeast Structural Genomics Consortium, Rutgers, the State University of New Jersey, Piscataway, New Jersey, 08854, USA
| | - Jeffrey L Mills
- Department of Chemistry, The State University of New York at Buffalo, and Northeast Structural Genomics Consortium, Buffalo, New York, 14260, USA
| | - Alexander F Montelione
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, and Northeast Structural Genomics Consortium, Rutgers, the State University of New Jersey, Piscataway, New Jersey, 08854, USA
| | - Kari Pederson
- Complex Carbohydrate Research Center and Northeast Structural Genomics Consortium, University of Georgia, Athens, Georgia, 30602, USA
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, USA
| | - Theresa Ramelot
- Department of Chemistry and Biochemistry, Northeast Structural Genomics Consortium, Miami University, Oxford, Ohio, 45056, USA
| | - Paolo Rossi
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, and Northeast Structural Genomics Consortium, Rutgers, the State University of New Jersey, Piscataway, New Jersey, 08854, USA
| | - Jayaraman Seetharaman
- Department of Biological Sciences and Northeast Structural Genomics Consortium, Columbia University, New York, NY, 10027, USA
| | - David Snyder
- Department of Chemistry, College of Science and Health, William Paterson University of NJ, Wayne, New Jersey, 07470, USA
| | - G V T Swapna
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, and Northeast Structural Genomics Consortium, Rutgers, the State University of New Jersey, Piscataway, New Jersey, 08854, USA
| | - Sergey M Vorobiev
- Department of Biological Sciences and Northeast Structural Genomics Consortium, Columbia University, New York, NY, 10027, USA
| | - Yibing Wu
- Department of Chemistry, The State University of New York at Buffalo, and Northeast Structural Genomics Consortium, Buffalo, New York, 14260, USA
| | - Rong Xiao
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, and Northeast Structural Genomics Consortium, Rutgers, the State University of New Jersey, Piscataway, New Jersey, 08854, USA
| | - Yunhuang Yang
- Department of Chemistry and Biochemistry, Northeast Structural Genomics Consortium, Miami University, Oxford, Ohio, 45056, USA
| | - Cheryl H Arrowsmith
- Cancer Genomics & Proteomics, Department of Medical Biophysics, Ontario Cancer Institute, and Northeast Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Canada
| | - John F Hunt
- Department of Biological Sciences and Northeast Structural Genomics Consortium, Columbia University, New York, NY, 10027, USA
| | - Michael A Kennedy
- Department of Chemistry and Biochemistry, Northeast Structural Genomics Consortium, Miami University, Oxford, Ohio, 45056, USA
| | - James H Prestegard
- Complex Carbohydrate Research Center and Northeast Structural Genomics Consortium, University of Georgia, Athens, Georgia, 30602, USA
| | - Thomas Szyperski
- Department of Chemistry, The State University of New York at Buffalo, and Northeast Structural Genomics Consortium, Buffalo, New York, 14260, USA
| | - Liang Tong
- Department of Biological Sciences and Northeast Structural Genomics Consortium, Columbia University, New York, NY, 10027, USA
| | - Gaetano T Montelione
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, and Northeast Structural Genomics Consortium, Rutgers, the State University of New Jersey, Piscataway, New Jersey, 08854, USA.,Department of Biochemistry, Robert Wood Johnson Medical School, Rutgers, the State University of New Jersey, Piscataway, New Jersey, 08854, USA
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Rosato A, Vranken W, Fogh RH, Ragan TJ, Tejero R, Pederson K, Lee HW, Prestegard JH, Yee A, Wu B, Lemak A, Houliston S, Arrowsmith CH, Kennedy M, Acton TB, Xiao R, Liu G, Montelione GT, Vuister GW. The second round of Critical Assessment of Automated Structure Determination of Proteins by NMR: CASD-NMR-2013. J Biomol NMR 2015; 62:413-24. [PMID: 26071966 PMCID: PMC4569658 DOI: 10.1007/s10858-015-9953-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Accepted: 05/28/2015] [Indexed: 05/21/2023]
Abstract
The second round of the community-wide initiative Critical Assessment of automated Structure Determination of Proteins by NMR (CASD-NMR-2013) comprised ten blind target datasets, consisting of unprocessed spectral data, assigned chemical shift lists and unassigned NOESY peak and RDC lists, that were made available in both curated (i.e. manually refined) or un-curated (i.e. automatically generated) form. Ten structure calculation programs, using fully automated protocols only, generated a total of 164 three-dimensional structures (entries) for the ten targets, sometimes using both curated and un-curated lists to generate multiple entries for a single target. The accuracy of the entries could be established by comparing them to the corresponding manually solved structure of each target, which was not available at the time the data were provided. Across the entire data set, 71 % of all entries submitted achieved an accuracy relative to the reference NMR structure better than 1.5 Å. Methods based on NOESY peak lists achieved even better results with up to 100% of the entries within the 1.5 Å threshold for some programs. However, some methods did not converge for some targets using un-curated NOESY peak lists. Over 90% of the entries achieved an accuracy better than the more relaxed threshold of 2.5 Å that was used in the previous CASD-NMR-2010 round. Comparisons between entries generated with un-curated versus curated peaks show only marginal improvements for the latter in those cases where both calculations converged.
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Affiliation(s)
- Antonio Rosato
- Department of Chemistry and Magnetic Resonance Center, University of Florence, 50019, Sesto Fiorentino, Italy
| | - Wim Vranken
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
- (IB)2 Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Triomflaan, 1050, Brussels, Belgium
| | - Rasmus H Fogh
- Department of Biochemistry, School of Biological Sciences, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester, LE1 9HN, UK
| | - Timothy J Ragan
- Department of Biochemistry, School of Biological Sciences, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester, LE1 9HN, UK
| | - Roberto Tejero
- Departamento de Química Física, Universidad de Valencia, Avda. Dr. Moliner 50, 46100, Burjassot (Valencia), Spain
| | - Kari Pederson
- Complex Carbohydrate Research Center and Northeast Structural Genomics Consortium, University of Georgia, Athens, GA, 30602, USA
| | - Hsiau-Wei Lee
- Complex Carbohydrate Research Center and Northeast Structural Genomics Consortium, University of Georgia, Athens, GA, 30602, USA
| | - James H Prestegard
- Complex Carbohydrate Research Center and Northeast Structural Genomics Consortium, University of Georgia, Athens, GA, 30602, USA
| | - Adelinda Yee
- Department of Medical Biophysics, Cancer Genomics and Proteomics, Ontario Cancer Institute, Northeast Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Bin Wu
- Department of Medical Biophysics, Cancer Genomics and Proteomics, Ontario Cancer Institute, Northeast Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Alexander Lemak
- Department of Medical Biophysics, Cancer Genomics and Proteomics, Ontario Cancer Institute, Northeast Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Scott Houliston
- Department of Medical Biophysics, Cancer Genomics and Proteomics, Ontario Cancer Institute, Northeast Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Cheryl H Arrowsmith
- Department of Medical Biophysics, Cancer Genomics and Proteomics, Ontario Cancer Institute, Northeast Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Michael Kennedy
- Department of Chemistry and Biochemistry, Northeast Structural Genomics Consortium, Miami University, Oxford, OH, 45056, USA
| | - Thomas B Acton
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| | - Rong Xiao
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| | - Gaohua Liu
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| | - Gaetano T Montelione
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA.
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA.
| | - Geerten W Vuister
- Department of Biochemistry, School of Biological Sciences, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester, LE1 9HN, UK.
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33
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Queiroz INL, Wang X, Glushka JN, Santos GRC, Valente AP, Prestegard JH, Woods RJ, Mourão PAS, Pomin VH. Impact of sulfation pattern on the conformation and dynamics of sulfated fucan oligosaccharides as revealed by NMR and MD. Glycobiology 2014; 25:535-47. [PMID: 25527427 DOI: 10.1093/glycob/cwu184] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Sulfated fucans from sea urchin egg jelly express well-defined chemical structures that vary with species. This species specificity regulates the sperm acrosome reaction, a critical step to assure intra-specific fertilization. In addition, these polysaccharides are involved in other biological activities such as anticoagulation. Although sulfation patterns are relevant to the levels of response in both activities, conformation and dynamics of these glycans are also contributing factors. However, data about these features of sulfated fucans are very rare. To address this, we have employed nuclear magnetic resonance experiments combined with molecular dynamics on structurally defined oligosaccharides derived from two sulfated fucans. The results have indicated that the oligosaccharides are flexible in solution. Ring conformation of their composing units displays just the (1)C4 chair configuration. In a particular octasaccharide, composed of two tetrasaccharide sequences, inter-residual hydrogen bonds play a role to decrease dynamics in these repeating units. Conversely, the linking disaccharide [-3)-α-L-Fucp-2(OSO3(-))-(1-3)-α-L-Fucp-4(OCO3(-))-(1-] located right between the two tetrasaccharide units has amplified motions suggested to be promoted by electrostatic repulsion of sulfates on opposite sides of the central glycosidic bond. This conjunction of information about conformation and dynamics of sulfated fucan oligosaccharides provides new insights to explain how these glycans behave free in solution and influenced by sulfation patterns. It may also serve for future studies concerning structure-function relationship of sulfated fucans, especially those involving sea urchin fertilization and anticoagulation.
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Affiliation(s)
- Ismael N L Queiroz
- Programa de Glicobiologia, Instituto de Bioquímica Médica Leopoldo de Meis, and Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-913, Brazil
| | - Xiaocong Wang
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - John N Glushka
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Gustavo R C Santos
- Programa de Glicobiologia, Instituto de Bioquímica Médica Leopoldo de Meis, and Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-913, Brazil
| | - Ana P Valente
- Centro Nacional de Ressonância Nuclear Magnética de Macromoléculas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brasil
| | - James H Prestegard
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Robert J Woods
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Paulo A S Mourão
- Programa de Glicobiologia, Instituto de Bioquímica Médica Leopoldo de Meis, and Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-913, Brazil
| | - Vitor H Pomin
- Programa de Glicobiologia, Instituto de Bioquímica Médica Leopoldo de Meis, and Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-913, Brazil
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34
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Lemak A, Wu B, Yee A, Houliston S, Lee HW, Gutmanas A, Fang X, Garcia M, Semesi A, Wang YX, Prestegard JH, Arrowsmith CH. Structural characterization of a flexible two-domain protein in solution using small angle X-ray scattering and NMR data. Structure 2014; 22:1862-1874. [PMID: 25456817 PMCID: PMC5046226 DOI: 10.1016/j.str.2014.09.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 09/10/2014] [Accepted: 09/12/2014] [Indexed: 01/09/2023]
Abstract
Multidomain proteins in which individual domains are connected by linkers often possess inherent interdomain flexibility that significantly complicates their structural characterization in solution using either nuclear magnetic resonance (NMR) spectroscopy or small-angle X-ray scattering (SAXS) alone. Here, we report a protocol for joint refinement of flexible multidomain protein structures against NMR distance and angular restraints, residual dipolar couplings, and SAXS data. The protocol is based on the ensemble optimization method principle (Bernadó et al., 2007) and is compared with different refinement strategies for the structural characterization of the flexible two-domain protein sf3636 from Shigella flexneri 2a. The results of our refinement suggest the existence of a dominant population of configurational states in solution possessing an overall elongated shape and restricted relative twisting of the two domains.
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Affiliation(s)
- Alexander Lemak
- Princess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada
| | - Bin Wu
- Princess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada
| | - Adelinda Yee
- Princess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada
| | - Scott Houliston
- Princess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada
| | - Hsiau-Wei Lee
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Aleksandras Gutmanas
- Princess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada
| | - Xianyang Fang
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, National Cancer Institute at Frederick, National Institutes of Health, Frederick, MD 21702, USA
| | - Maite Garcia
- Princess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada
| | - Anthony Semesi
- Princess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada
| | - Yun-Xing Wang
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, National Cancer Institute at Frederick, National Institutes of Health, Frederick, MD 21702, USA
| | - James H Prestegard
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Cheryl H Arrowsmith
- Princess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada.
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Pulavarti SVSRK, Huang YJ, Pederson K, Acton TB, Xiao R, Everett JK, Prestegard JH, Montelione GT, Szyperski T. Solution NMR structures of immunoglobulin-like domains 7 and 12 from obscurin-like protein 1 contribute to the structural coverage of the Human Cancer Protein Interaction Network. J Struct Funct Genomics 2014; 15:209-214. [PMID: 24989974 PMCID: PMC4945113 DOI: 10.1007/s10969-014-9185-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 06/14/2014] [Indexed: 06/03/2023]
Abstract
High-quality solution NMR structures of immunoglobulin-like domains 7 and 12 from human obscurin-like protein 1 were solved. The two domains share 30% sequence identity and their structures are, as expected, rather similar. The new structures contribute to structural coverage of human cancer associated proteins. Mutations of Arg 812 in domain 7 cause the rare 3-M syndrome, and this site is located in a surface area predicted to be involved in protein-protein interactions.
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Affiliation(s)
- Surya VSRK Pulavarti
- Department of Chemistry, The State University of New York at Buffalo, and Northeast Structural Genomics Consortium, Buffalo, NY 14260, USA
| | - Yuanpeng J. Huang
- Center of Advanced Biotechnology and Medicine and Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey and Northeast Structural Genomics Consortium, Piscataway, NJ 08854, USA
| | - Kari Pederson
- Complex Carbohydrate Research Center, University of Georgia, and Northeast Structural Genomics Consortium, Athens, GA 30602, USA
| | - Thomas B. Acton
- Center of Advanced Biotechnology and Medicine and Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey and Northeast Structural Genomics Consortium, Piscataway, NJ 08854, USA
| | - Rong Xiao
- Center of Advanced Biotechnology and Medicine and Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey and Northeast Structural Genomics Consortium, Piscataway, NJ 08854, USA
| | - John K. Everett
- Center of Advanced Biotechnology and Medicine and Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey and Northeast Structural Genomics Consortium, Piscataway, NJ 08854, USA
| | - James H. Prestegard
- Complex Carbohydrate Research Center, University of Georgia, and Northeast Structural Genomics Consortium, Athens, GA 30602, USA
| | - Gaetano T. Montelione
- Center of Advanced Biotechnology and Medicine and Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey and Northeast Structural Genomics Consortium, Piscataway, NJ 08854, USA
| | - Thomas Szyperski
- Department of Chemistry, The State University of New York at Buffalo, and Northeast Structural Genomics Consortium, Buffalo, NY 14260, USA
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36
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Yang Y, Ramelot TA, Lee HW, Xiao R, Everett JK, Montelione GT, Prestegard JH, Kennedy MA. Solution structure of a C-terminal fragment (175-257) of CV_0373 protein from Chromobacterium violaceum adopts a winged helix-turn-helix (wHTH) fold. J Biomol NMR 2014; 60:197-202. [PMID: 25270885 PMCID: PMC4928572 DOI: 10.1007/s10858-014-9860-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 08/28/2014] [Indexed: 06/03/2023]
Affiliation(s)
- Yunhuang Yang
- Department of Chemistry and Biochemistry, and the Northeast Structural Genomics Consortium, Miami University, Oxford, OH 45056, USA
| | - Theresa A. Ramelot
- Department of Chemistry and Biochemistry, and the Northeast Structural Genomics Consortium, Miami University, Oxford, OH 45056, USA
| | - Hsiau-Wei Lee
- Complex Carbohydrate Research Center, and the Northeast Structural Genomics Consortium, University of Georgia, Athens, GA 30602, USA
| | - Rong Xiao
- Department of Molecular Biology and Biochemistry, and the Northeast Structural Genomics Consortium, Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - John K. Everett
- Department of Molecular Biology and Biochemistry, and the Northeast Structural Genomics Consortium, Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Gaetano T. Montelione
- Department of Molecular Biology and Biochemistry, and the Northeast Structural Genomics Consortium, Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA. Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, NJ 08854, USA
| | - James H. Prestegard
- Complex Carbohydrate Research Center, and the Northeast Structural Genomics Consortium, University of Georgia, Athens, GA 30602, USA
| | - Michael A. Kennedy
- Department of Chemistry and Biochemistry, and the Northeast Structural Genomics Consortium, Miami University, Oxford, OH 45056, USA
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37
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Yang Y, Ramelot TA, Lee HW, Xiao R, Everett JK, Montelione GT, Prestegard JH, Kennedy MA. Solution structure of the free Zα domain of human DLM-1 (ZBP1/DAI), a Z-DNA binding domain. J Biomol NMR 2014; 60:189-95. [PMID: 25173411 PMCID: PMC4527548 DOI: 10.1007/s10858-014-9858-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 08/22/2014] [Indexed: 05/17/2023]
Affiliation(s)
- Yunhuang Yang
- Department of Chemistry and Biochemistry, and the Northeast Structural Genomics Consortium, Miami University, Oxford, Ohio, USA, 45056, United States
| | - Theresa A. Ramelot
- Department of Chemistry and Biochemistry, and the Northeast Structural Genomics Consortium, Miami University, Oxford, Ohio, USA, 45056, United States
| | - Hsiau-Wei Lee
- Complex Carbohydrate Research Center, and the Northeast Structural Genomics Consortium, University of Georgia, Athens, Georgia, USA, 30602, United States
| | - Rong Xiao
- Department of Molecular Biology and Biochemistry, and the Northeast Structural Genomics Consortium, Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - John K. Everett
- Department of Molecular Biology and Biochemistry, and the Northeast Structural Genomics Consortium, Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Gaetano T. Montelione
- Department of Molecular Biology and Biochemistry, and the Northeast Structural Genomics Consortium, Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
- Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, New Jersey 08854, United States
| | - James H. Prestegard
- Complex Carbohydrate Research Center, and the Northeast Structural Genomics Consortium, University of Georgia, Athens, Georgia, USA, 30602, United States
| | - Michael A. Kennedy
- Department of Chemistry and Biochemistry, and the Northeast Structural Genomics Consortium, Miami University, Oxford, Ohio, USA, 45056, United States
- Correspondence to: Michael A. Kennedy, Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, Phone: +1 523 529 8267, Fax: +1 513 529 5715,
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38
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Zhang C, Zhuo Y, Moniz HA, Wang S, Moremen KW, Prestegard JH, Brown EM, Yang JJ. Direct determination of multiple ligand interactions with the extracellular domain of the calcium-sensing receptor. J Biol Chem 2014; 289:33529-42. [PMID: 25305020 DOI: 10.1074/jbc.m114.604652] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Numerous in vivo functional studies have indicated that the dimeric extracellular domain (ECD) of the CaSR plays a crucial role in regulating Ca(2+) homeostasis by sensing Ca(2+) and l-Phe. However, direct interaction of Ca(2+) and Phe with the ECD of the receptor and the resultant impact on its structure and associated conformational changes have been hampered by the large size of the ECD, its high degree of glycosylation, and the lack of biophysical methods to monitor weak interactions in solution. In the present study, we purified the glycosylated extracellular domain of calcium-sensing receptor (CaSR) (ECD) (residues 20-612), containing either complex or high mannose N-glycan structures depending on the host cell line employed for recombinant expression. Both glycosylated forms of the CaSR ECD were purified as dimers and exhibit similar secondary structures with ∼ 50% α-helix, ∼ 20% β-sheet content, and a well buried Trp environment. Using various spectroscopic methods, we have shown that both protein variants bind Ca(2+) with a Kd of 3.0-5.0 mm. The local conformational changes of the proteins induced by their interactions with Ca(2+) were visualized by NMR with specific (15)N Phe-labeled forms of the ECD. Saturation transfer difference NMR approaches demonstrated for the first time a direct interaction between the CaSR ECD and l-Phe. We further demonstrated that l-Phe increases the binding affinity of the CaSR ECD for Ca(2+). Our findings provide new insights into the mechanisms by which Ca(2+) and amino acids regulate the CaSR and may pave the way for exploration of the structural properties of CaSR and other members of family C of the GPCR superfamily.
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Affiliation(s)
- Chen Zhang
- From the Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303
| | - You Zhuo
- From the Department of Chemistry
| | - Heather A Moniz
- the Department of Biochemistry and Molecular Biology and the Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, and
| | - Shuo Wang
- the Department of Biochemistry and Molecular Biology and the Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, and
| | - Kelley W Moremen
- the Department of Biochemistry and Molecular Biology and the Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, and
| | - James H Prestegard
- the Department of Biochemistry and Molecular Biology and the Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, and
| | - Edward M Brown
- the Department of Medicine, Division of Endocrinology, Brigham and Women's Hospital, Boston, Massachusetts 02115
| | - Jenny J Yang
- From the Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303,
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39
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Abstract
Dendritic cell-specific intracellular adhesion molecule-3-grabbing nonintegrin (DC-SIGN) is a C-type lectin highly expressed on the surface of antigen-presenting dendritic cells. DC-SIGN mediates interactions among dendritic cells, pathogens, and a variety of epithelia, myeloid cells, and endothelia by binding to high mannose residues on pathogenic invaders or fucosylated residues on the membranes of other immune cells. Although these interactions are normally beneficial, they can also contribute to disease. The structural characterization of binding geometries is therefore of interest as a basis for the construction of mimetics that can mediate the effects of abnormal immune response. Here, we report the structural characteristics of the interaction of the DC-SIGN carbohydrate recognition domain (CRD) with a common fucosylated entity, the Lewis(X) trisaccharide (Le(X)), using NMR methods. Titration of the monomeric DC-SIGN CRD with Le(X) monitored by 2D NMR revealed significant perturbations of DC-SIGN cross-peak positions in (1)H-(15)N heteronuclear single quantum coherence (HSQC) spectra and identified residues near the binding site. Additionally, saturation transfer difference (STD) and transferred nuclear Overhauser effect (trNOE) NMR experiments, using a tetrameric form of DC-SIGN, identified binding epitopes and bound conformations of the Le(X) ligand. The restraints derived from these multiple experiments were used to generate models for the binding of Le(X) to the DC-SIGN CRD. Ranking of the models based on the fit of model-based simulations of the trNOE data and STD buildup curves suggested conformations distinct from those seen in previous crystal structures. The new conformations offer insight into how differences between binding of Lewis(X) and mannose-terminated saccharides may be propagated.
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Affiliation(s)
- Kari Pederson
- Complex Carbohydrate Research Center, University of Georgia , Athens, Georgia 30602, United States
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40
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Prestegard JH, Agard DA, Moremen KW, Lavery LA, Morris LC, Pederson K. Sparse labeling of proteins: structural characterization from long range constraints. J Magn Reson 2014; 241:32-40. [PMID: 24656078 PMCID: PMC3964372 DOI: 10.1016/j.jmr.2013.12.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2013] [Revised: 12/17/2013] [Accepted: 12/19/2013] [Indexed: 05/07/2023]
Abstract
Structural characterization of biologically important proteins faces many challenges associated with degradation of resolution as molecular size increases and loss of resolution improving tools such as perdeuteration when non-bacterial hosts must be used for expression. In these cases, sparse isotopic labeling (single or small subsets of amino acids) combined with long range paramagnetic constraints and improved computational modeling offer an alternative. This perspective provides a brief overview of this approach and two discussions of potential applications; one involving a very large system (an Hsp90 homolog) in which perdeuteration is possible and methyl-TROSY sequences can potentially be used to improve resolution, and one involving ligand placement in a glycosylated protein where resolution is achieved by single amino acid labeling (the sialyltransferase, ST6Gal1). This is not intended as a comprehensive review, but as a discussion of future prospects that promise impact on important questions in the structural biology area.
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Affiliation(s)
- James H Prestegard
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, United States.
| | - David A Agard
- The Howard Hughes Medical Institute, Dept. Biochem. & Biophys., Univ. Calif. San Francisco, San Francisco, CA 94158, United States
| | - Kelley W Moremen
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, United States
| | - Laura A Lavery
- The Howard Hughes Medical Institute, Dept. Biochem. & Biophys., Univ. Calif. San Francisco, San Francisco, CA 94158, United States
| | - Laura C Morris
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, United States
| | - Kari Pederson
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, United States
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41
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Liu Y, Kahn RA, Prestegard JH. Interaction of Fapp1 with Arf1 and PI4P at a membrane surface: an example of coincidence detection. Structure 2014; 22:421-30. [PMID: 24462251 PMCID: PMC3951685 DOI: 10.1016/j.str.2013.12.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 12/23/2013] [Accepted: 12/28/2013] [Indexed: 10/25/2022]
Abstract
Interactions among ADP-ribosylation factors (ARFs), various adaptor proteins, and membrane lipids are essential for intracellular vesicle transport of a variety of cellular materials. Here, we present nuclear magnetic resonance (NMR)-based information on the nature of the interaction of yeast Arf1 (yArf1) and the pleckstrin homology (PH) domain of four-phosphate-adaptor protein 1 (Fapp1) as it occurs at a model membrane surface. Interactions favor a model in which Fapp1 is partially embedded in the membrane and interacts with a membrane-associated Arf1 molecule primarily through contacts between residues in switch I of Arf1 and regions near and under the solution exposed C-terminal extension of the PH domain. The Arf1 binding site on Fapp1-PH is distinct from a positively charged phosphatidylinositol-4-phosphate (PI4P) binding site. A structural model is constructed that supports coincidence detection of both activated ARF and PI4P as a mechanism facilitating Fapp1 recruitment to membranes.
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Affiliation(s)
- Yizhou Liu
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Richard A Kahn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA.
| | - James H Prestegard
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA.
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42
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Pulavarti SVSRK, Eletsky A, Lee HW, Acton TB, Xiao R, Everett JK, Prestegard JH, Montelione GT, Szyperski T. Solution NMR structure of CD1104B from pathogenic Clostridium difficile reveals a distinct α-helical architecture and provides first structural representative of protein domain family PF14203. J Struct Funct Genomics 2013; 14:155-160. [PMID: 24048810 PMCID: PMC3844015 DOI: 10.1007/s10969-013-9164-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 09/10/2013] [Indexed: 05/30/2023]
Abstract
A high-quality structure of the 68-residue protein CD1104B from Clostridium difficile strain 630 exhibits a distinct all α-helical fold. The structure presented here is the first representative of bacterial protein domain family PF14203 (currently 180 members) of unknown function (DUF4319) and reveals that the side-chains of the only two strictly conserved residues (Glu 8 and Lys 48) form a salt bridge. Moreover, these two residues are located in the vicinity of the largest surface cleft which is predicted to contribute to a surface area involved in protein-protein interactions. This, along with its coding in transposon CTn4, suggests that CD1104B (and very likely all members of Pfam 14203) functions by interacting with other proteins required for the transfer of transposons between different bacterial species.
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Affiliation(s)
- Surya VSRK Pulavarti
- Department of Chemistry, The State University of New York at Buffalo, and Northeast Structural Genomics Consortium, Buffalo, NY 14260, USA
| | - Alexander Eletsky
- Department of Chemistry, The State University of New York at Buffalo, and Northeast Structural Genomics Consortium, Buffalo, NY 14260, USA
| | - Hsiau-Wei Lee
- Complex Carbohydrate Research Center, University at Georgia, and Northeast Structural Genomics Consortium, Athens, GA 30602, USA
| | - Thomas B. Acton
- Center of Advanced Biotechnology and Medicine and Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey and Northeast Structural Genomics Consortium, Piscataway, NJ 08854, USA
| | - Rong Xiao
- Center of Advanced Biotechnology and Medicine and Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey and Northeast Structural Genomics Consortium, Piscataway, NJ 08854, USA
| | - John K. Everett
- Center of Advanced Biotechnology and Medicine and Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey and Northeast Structural Genomics Consortium, Piscataway, NJ 08854, USA
| | - James H. Prestegard
- Complex Carbohydrate Research Center, University at Georgia, and Northeast Structural Genomics Consortium, Athens, GA 30602, USA
| | - Gaetano T. Montelione
- Center of Advanced Biotechnology and Medicine and Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey and Northeast Structural Genomics Consortium, Piscataway, NJ 08854, USA, Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, UMDNJ, Piscataway NJ 08854, USA
| | - Thomas Szyperski
- Department of Chemistry, The State University of New York at Buffalo, and Northeast Structural Genomics Consortium, Buffalo, NY 14260, USA
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43
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Prestegard JH, Sahu SC, Nkari WK, Morris LC, Live D, Gruta C. Chemical shift prediction for denatured proteins. J Biomol NMR 2013; 55:201-9. [PMID: 23297019 PMCID: PMC3570700 DOI: 10.1007/s10858-012-9702-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Accepted: 12/23/2012] [Indexed: 05/23/2023]
Abstract
While chemical shift prediction has played an important role in aspects of protein NMR that include identification of secondary structure, generation of torsion angle constraints for structure determination, and assignment of resonances in spectra of intrinsically disordered proteins, interest has arisen more recently in using it in alternate assignment strategies for crosspeaks in (1)H-(15)N HSQC spectra of sparsely labeled proteins. One such approach involves correlation of crosspeaks in the spectrum of the native protein with those observed in the spectrum of the denatured protein, followed by assignment of the peaks in the latter spectrum. As in the case of disordered proteins, predicted chemical shifts can aid in these assignments. Some previously developed empirical formulas for chemical shift prediction have depended on basis data sets of 20 pentapeptides. In each case the central residue was varied among the 20 amino common acids, with the flanking residues held constant throughout the given series. However, previous choices of solvent conditions and flanking residues make the parameters in these formulas less than ideal for general application to denatured proteins. Here, we report (1)H and (15)N shifts for a set of alanine based pentapeptides under the low pH urea denaturing conditions that are more appropriate for sparse label assignments. New parameters have been derived and a Perl script was created to facilitate comparison with other parameter sets. A small, but significant, improvement in shift predictions for denatured ubiquitin is demonstrated.
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44
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Barb AW, Wang X, Prestegard JH. Refolded recombinant Siglec5 for NMR investigation of complex carbohydrate binding. Protein Expr Purif 2013; 88:183-9. [PMID: 23321067 DOI: 10.1016/j.pep.2013.01.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 01/02/2013] [Accepted: 01/03/2013] [Indexed: 11/26/2022]
Abstract
Sialic-acid-binding immunoglobulin-like lectin (Siglec5) is a carbohydrate-binding surface receptor expressed on neutrophils, monocytes and B cells in human lymphoid and myeloid cell lineages. Existing structural and functional data fail to define the clear ligand specificity of Siglec5, though like other Siglec family members, it binds a variety of complex carbohydrates containing a sialic acid at the non-reducing terminus. Prokaryotic expression of this protein has proven challenging due to disulfide bonds and Asn-linked glycosylation. We developed an expression and purification protocol that uses an on-column strategy to refold Escherichia coli expressed protein that produced a high yield (2 mg/L) of the single N-terminal Siglec5 carbohydrate recognition domain (CRD). A 2D heteronuclear single-quantum coherence (HSQC) nuclear magnetic resonance (NMR) spectrum showed this material was folded, and a secondary structure prediction based on the assigned chemical shifts of backbone atoms was consistent with a previously determined X-ray model. NMR chemical shift mapping of Siglec5 binding to three carbohydrate ligands revealed similarities in binding interfaces and affinities. In addition, the role of alternate protein conformations identified by NMR in ligand binding is discussed. These studies demonstrate the Siglec5 CRD alone is sufficient for binding sialylated carbohydrates and provide a foundation for further investigation of Siglec5 structure and function.
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Affiliation(s)
- Adam W Barb
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
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45
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Eletsky A, Jeong MY, Kim H, Lee HW, Xiao R, Pagliarini DJ, Prestegard JH, Winge DR, Montelione GT, Szyperski T. Solution NMR structure of yeast succinate dehydrogenase flavinylation factor Sdh5 reveals a putative Sdh1 binding site. Biochemistry 2012; 51:8475-7. [PMID: 23062074 PMCID: PMC3667956 DOI: 10.1021/bi301171u] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The yeast mitochondrial protein Sdh5 is required for the covalent attachment of flavin adenine dinucleotide (FAD) to protein Sdh1, a subunit of the heterotetrameric enzyme succinate dehydrogenase. The NMR structure of Sdh5 represents the first eukaryotic structure of Pfam family PF03937 and reveals a conserved surface region, which likely represents a putative Sdh1-Sdh5 interaction interface. Point mutations in this region result in the loss of covalent flavinylation of Sdh1. Moreover, chemical shift perturbation measurements showed that Sdh5 does not bind FAD in vitro, indicating that it is not a simple cofactor transporter in vivo.
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Affiliation(s)
- Alexander Eletsky
- Department of Chemistry, The State University of New York at Buffalo, Buffalo, New York 14260, United States
- Northeast Structural Genomics Consortium Supporting Information Placeholder
| | - Mi-Young Jeong
- University of Utah Health Sciences Center, Departments of Medicine and Biochemistry and Mitochondrial Proteome Partnership, Salt Lake City, Utah 84132, United States
| | - Hyung Kim
- University of Utah Health Sciences Center, Departments of Medicine and Biochemistry and Mitochondrial Proteome Partnership, Salt Lake City, Utah 84132, United States
| | - Hsiau-Wei Lee
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
- Northeast Structural Genomics Consortium Supporting Information Placeholder
| | - Rong Xiao
- Center of Advanced Biotechnology and Medicine and Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey and Department of Biochemistry, Robert Wood Johnson Medical School, UMDNJ, Piscataway, New Jersey 08854, United States
- Northeast Structural Genomics Consortium Supporting Information Placeholder
| | - David J. Pagliarini
- Department of Biochemistry and the Mitochondrial Protein Partnership, The University of Wisconsin – Madison, Madison, Wisconsin 53562, United States
| | - James H. Prestegard
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
- Northeast Structural Genomics Consortium Supporting Information Placeholder
| | - Dennis R. Winge
- University of Utah Health Sciences Center, Departments of Medicine and Biochemistry and Mitochondrial Proteome Partnership, Salt Lake City, Utah 84132, United States
| | - Gaetano T. Montelione
- Center of Advanced Biotechnology and Medicine and Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey and Department of Biochemistry, Robert Wood Johnson Medical School, UMDNJ, Piscataway, New Jersey 08854, United States
- Northeast Structural Genomics Consortium Supporting Information Placeholder
| | - Thomas Szyperski
- Department of Chemistry, The State University of New York at Buffalo, Buffalo, New York 14260, United States
- Northeast Structural Genomics Consortium Supporting Information Placeholder
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46
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Ramelot TA, Rossi P, Forouhar F, Lee HW, Yang Y, Ni S, Unser S, Lew S, Seetharaman J, Xiao R, Acton TB, Everett JK, Prestegard JH, Hunt JF, Montelione GT, Kennedy MA. Structure of a specialized acyl carrier protein essential for lipid A biosynthesis with very long-chain fatty acids in open and closed conformations. Biochemistry 2012; 51:7239-49. [PMID: 22876860 DOI: 10.1021/bi300546b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The solution nuclear magnetic resonance (NMR) structures and backbone (15)N dynamics of the specialized acyl carrier protein (ACP), RpAcpXL, from Rhodopseudomonas palustris, in both the apo form and holo form modified by covalent attachment of 4'-phosphopantetheine at S37, are virtually identical, monomeric, and correspond to the closed conformation. The structures have an extra α-helix compared to the archetypical ACP from Escherichia coli, which has four helices, resulting in a larger opening to the hydrophobic cavity. Chemical shift differences between apo- and holo-RpAcpXL indicated some differences in the hinge region between α2 and α3 and in the hydrophobic cavity environment, but corresponding changes in nuclear Overhauser effect cross-peak patterns were not detected. In contrast to the NMR structures, apo-RpAcpXL was observed in an open conformation in crystals that diffracted to 2.0 Å resolution, which resulted from movement of α3. On the basis of the crystal structure, the predicted biological assembly is a homodimer. Although the possible biological significance of dimerization is unknown, there is potential that the resulting large shared hydrophobic cavity could accommodate the very long-chain fatty acid (28-30 carbons) that this specialized ACP is known to synthesize and transfer to lipid A. These structures are the first representatives of the AcpXL family and the first to indicate that dimerization may be important for the function of these specialized ACPs.
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Affiliation(s)
- Theresa A Ramelot
- Department of Chemistry and Biochemistry, Northeast Structural Genomics Consortium, Miami University, Oxford, Ohio 45056, United States.
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47
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Barb AW, Ho TG, Flanagan-Steet H, Prestegard JH. Lanthanide binding and IgG affinity construct: potential applications in solution NMR, MRI, and luminescence microscopy. Protein Sci 2012; 21:1456-66. [PMID: 22851279 DOI: 10.1002/pro.2133] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Revised: 07/16/2012] [Accepted: 07/17/2012] [Indexed: 11/06/2022]
Abstract
Paramagnetic lanthanide ions when bound to proteins offer great potential for structural investigations that utilize solution nuclear magnetic resonance spectroscopy, magnetic resonance imaging, or optical microscopy. However, many proteins do not have native metal ion binding sites and engineering a chimeric protein to bind an ion while retaining affinity for a protein of interest represents a significant challenge. Here we report the characterization of an immunoglobulin G-binding protein redesigned to include a lanthanide binding motif in place of a loop between two helices (Z-L2LBT). It was shown to bind Tb³⁺ with 130 nM affinity. Ions such as Dy³⁺, Yb³⁺, and Ce³⁺ produce paramagnetic effects on NMR spectra and the utility of these effects is illustrated by their use in determining a structural model of the metal-complexed Z-L2LBT protein and a preliminary characterization of the dynamic distribution of IgG Fc glycan positions. Furthermore, this designed protein is demonstrated to be a novel IgG-binding reagent for magnetic resonance imaging (Z-L2LBT:Gd³⁺ complex) and luminescence microscopy (Z-L2LBT: Tb³⁺ complex).
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Affiliation(s)
- Adam W Barb
- Complex Carbohydrate Research Center, The University of Georgia, Athens, Georgia, USA
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48
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Barb AW, Meng L, Gao Z, Johnson RW, Moremen KW, Prestegard JH. NMR characterization of immunoglobulin G Fc glycan motion on enzymatic sialylation. Biochemistry 2012; 51:4618-26. [PMID: 22574931 DOI: 10.1021/bi300319q] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The terminal carbohydrate residues of the N-glycan on the immunoglobulin G (IgG) fragment crystallizable (Fc) determine whether IgG activates pro- or anti-inflammatory receptors. The IgG Fc alone becomes potently anti-inflammatory upon addition of α2-6-linked N-acetylneuraminic acid residues to the N-glycan, stimulating interest in use of this entity in novel therapies for autoimmune disease [Kaneko et al. (2006) Science313, 670-3]. Complete Fc sialylation has, however, been deemed challenging due to a combination of branch specificity and perceived protection by glycan-protein interactions. Here we report the preparation of high levels of disialylated Fc by using sufficient amounts of a highly active α2-6 sialyltransferase (ST6Gal1) preparation expressed in a transiently transformed human cell culture. Surprisingly, ST6Gal1 sialylated the two termini of the complex-type binantennary glycan in a manner remarkably similar to that observed for the free N-glycan, suggesting the Fc polypeptide does not greatly influence ST6Gal1 specificity. In addition, sialylation of either branch terminus does not appear to dramatically alter the motional behavior of the N-glycan as judged by solution NMR spectroscopy. Together these, data suggest the N-glycan occupies two distinct states: one with both glycan termini sequestered from enzymatic modification by an α1-6Man-branch interaction with the polypeptide surface and the other with both glycan termini exposed to the bulk solvent and free from glycan-polypeptide interactions. The results suggest new modes by which disialylated Fc can act as an anti-inflammatory effector.
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Affiliation(s)
- Adam W Barb
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
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49
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Ertekin A, Aramini JM, Rossi P, Leonard PG, Janjua H, Xiao R, Maglaqui M, Lee HW, Prestegard JH, Montelione GT. Human cyclin-dependent kinase 2-associated protein 1 (CDK2AP1) is dimeric in its disulfide-reduced state, with natively disordered N-terminal region. J Biol Chem 2012; 287:16541-9. [PMID: 22427660 DOI: 10.1074/jbc.m112.343863] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
CDK2AP1 (cyclin-dependent kinase 2-associated protein 1), corresponding to the gene doc-1 (deleted in oral cancer 1), is a tumor suppressor protein. The doc-1 gene is absent or down-regulated in hamster oral cancer cells and in many other cancer cell types. The ubiquitously expressed CDK2AP1 protein is the only known specific inhibitor of CDK2, making it an important component of cell cycle regulation during G(1)-to-S phase transition. Here, we report the solution structure of CDK2AP1 by combined methods of solution state NMR and amide hydrogen/deuterium exchange measurements with mass spectrometry. The homodimeric structure of CDK2AP1 includes an intrinsically disordered 60-residue N-terminal region and a four-helix bundle dimeric structure with reduced Cys-105 in the C-terminal region. The Cys-105 residues are, however, poised for disulfide bond formation. CDK2AP1 is phosphorylated at a conserved Ser-46 site in the N-terminal "intrinsically disordered" region by IκB kinase ε.
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Affiliation(s)
- Asli Ertekin
- Center for Advanced Biotechnology and Medicine and Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
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50
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Eletsky A, Petrey D, Cliff Zhang Q, Lee HW, Acton TB, Xiao R, Everett JK, Prestegard JH, Honig B, Montelione GT, Szyperski T. Solution NMR structures reveal unique homodimer formation by a winged helix-turn-helix motif and provide first structures for protein domain family PF10771. J Struct Funct Genomics 2012; 13:1-7. [PMID: 22223187 PMCID: PMC3654790 DOI: 10.1007/s10969-011-9121-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Accepted: 12/13/2011] [Indexed: 11/29/2022]
Abstract
High-quality NMR structures of the homo-dimeric proteins Bvu3908 (69-residues in monomeric unit) from Bacteroides vulgatus and Bt2368 (74-residues) from Bacteroides thetaiotaomicron reveal the presence of winged helix-turn-helix (wHTH) motifs mediating tight complex formation. Such homo-dimer formation by winged HTH motifs is otherwise found only in two DNA-binding proteins with known structure: the C-terminal wHTH domain of transcriptional activator FadR from E. coli and protein TubR from B. thurigensis, which is involved in plasmid DNA segregation. However, the relative orientation of the wHTH motifs is different and residues involved in DNA-binding are not conserved in Bvu3908 and Bt2368. Hence, the proteins of the present study are not very likely to bind DNA, but are likely to exhibit a function that has thus far not been ascribed to homo-dimers formed by winged HTH motifs. The structures of Bvu3908 and Bt2368 are the first atomic resolution structures for PFAM family PF10771, a family of unknown function (DUF2582) currently containing 128 members.
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Affiliation(s)
- Alexander Eletsky
- Department of Chemistry, The State University of New York at Buffalo, and Northeast Structural Genomics Consortium, Buffalo, NY 14260, USA
| | - Donald Petrey
- Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Center for Computational Biology and Bioinformatics, Columbia University, New York, NY 10032, USA
| | - Qiangfeng Cliff Zhang
- Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Center for Computational Biology and Bioinformatics, Columbia University, New York, NY 10032, USA
| | - Hsiau-Wei Lee
- Complex Carbohydrate Research Center, University of Georgia, and Northeast Structural Genomics Consortium, Athens, GA 30602, USA
| | - Thomas B. Acton
- Department of Molecular Biology and Biochemistry, Center of Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Department of Biochemistry, Robert Wood Johnson Medical School, UMDNJ, and Northeast Structural Genomics Consortium, Piscataway, NJ 08854, USA
| | - Rong Xiao
- Department of Molecular Biology and Biochemistry, Center of Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Department of Biochemistry, Robert Wood Johnson Medical School, UMDNJ, and Northeast Structural Genomics Consortium, Piscataway, NJ 08854, USA
| | - John K. Everett
- Department of Molecular Biology and Biochemistry, Center of Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Department of Biochemistry, Robert Wood Johnson Medical School, UMDNJ, and Northeast Structural Genomics Consortium, Piscataway, NJ 08854, USA
| | - James H. Prestegard
- Complex Carbohydrate Research Center, University of Georgia, and Northeast Structural Genomics Consortium, Athens, GA 30602, USA
| | - Barry Honig
- Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Center for Computational Biology and Bioinformatics, Columbia University, New York, NY 10032, USA
| | - Gaetano T. Montelione
- Department of Molecular Biology and Biochemistry, Center of Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Department of Biochemistry, Robert Wood Johnson Medical School, UMDNJ, and Northeast Structural Genomics Consortium, Piscataway, NJ 08854, USA
| | - Thomas Szyperski
- Department of Chemistry, The State University of New York at Buffalo, and Northeast Structural Genomics Consortium, Buffalo, NY 14260, USA
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