AssignSLP_GUI, a software tool exploiting AI for NMR resonance assignment of sparsely labeled proteins

Williams, Robert V.; Rogals, Monique J.; Eletsky, Alexander; Huang, Chin‐Cheng; Morris, Laura C.; Moremen, Kelley W.; Prestegard, James H.

doi:10.1016/j.jmr.2022.107336

Cited by 5 publications

(16 citation statements)

References 52 publications

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“…Man 5 GlcNAc 2 glycans were added using tools available in the GLYCAM website (). This initial structure was solvated in TIP5P water and subjected to a 1 μs GaMD trajectory as described generally in the AMBER20 manual and more specifically in our previously submitted publication . The TIP5P water model, as opposed to the more computationally efficient TIP3P model, was chosen to avoid an overemphasis of protein–glycan interactions that had been noted previously. , …”

Section: Resultsmentioning

confidence: 99%

“…This initial structure was solvated in TIP5P water and subjected to a 1 μs GaMD trajectory as described generally in the AMBER20 manual 31 and more specifically in our previously submitted publication. 20 The TIP5P water model, as opposed to the more computationally efficient TIP3P model, was chosen to avoid an overemphasis of protein−glycan interactions that had been noted previously. 8,10 To extract a set of glycan conformers small enough to test against experimental observation, we clustered the GaMD frames based on a root mean square deviation (rmsd) of the position of central ring atoms (C1, C2, C4, C5) of all of the glycan residues on proteins aligned pairwise frame by frame for every tenth frame.…”

Section: ■ Resultsmentioning

confidence: 99%

“…Our approach for the target discussed here has recently been described, along with a resonance assignment strategy for proteins sparsely labeled with NMR-active isotopes. 20 The protein target we select for glycan conformational analysis is the N-terminal domain of human Carcinoembryonic Antigen Cell Adhesion Molecule 1, hCEACAM1. hCEACAM1 is a highly glycosylated extracellular protein receptor, which has been implicated in gastrointestinal autoimmune disorders, cancer, and host−pathogen interactions.…”

Section: ■ Introductionmentioning

confidence: 99%

“…This stops N -glycan processing at the Man 5 GlcNAc 2 stage, yielding a homogeneous complement of glycoforms. , This falls short of the longer glycans natively present, but it would be much more difficult to achieve homogeneity of these complex glycans, and the shorter glycans will provide some insight into the nature of glycan–protein interactions. The disulfide bond included in the lanthanide-binding peptide both stabilizes the structure and raises occupancy of the three N -glycan sites to ∼90% …”

Section: Introductionmentioning

confidence: 99%

“…However, choosing sites for the addition that neither distorts native protein structure nor reduces binding affinities of the loop must be done carefully. Our approach for the target discussed here has recently been described, along with a resonance assignment strategy for proteins sparsely labeled with NMR-active isotopes …”

Section: Introductionmentioning

confidence: 99%

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Glycan Conformation in the Heavily Glycosylated Protein, CEACAM1

et al. 2022

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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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Section: Resultsmentioning

confidence: 99%

Section: ■ Resultsmentioning

confidence: 99%

Section: ■ Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Glycan Conformation in the Heavily Glycosylated Protein, CEACAM1

et al. 2022

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Nuclear magnetic resonance‐based structural elucidation of novel marine glycans and derived oligosaccharides

Dwivedi

Maurya

Ahmed

et al. 2023

Magnetic Reson in Chemistry

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Marine glycans of defined structures are unique representatives among all kinds of structurally complex glycans endowed with important biological actions. Besides their unique biological properties, these marine sugars also enable advanced structure–activity relationship (SAR) studies given their distinct and defined structures. However, the natural high molecular weights (MWs) of these marine polysaccharides, sometimes even bigger than 100 kDa, pose a problem in many biophysical and analytical studies. Hence, the preparation of low MW oligosaccharides becomes a strategy to overcome the problem. Regardless of the polymeric or oligomeric lengths of these molecules, structural elucidation is mandatory for SAR studies. For this, nuclear magnetic resonance (NMR) spectroscopy plays a pivotal role. Here, we revisit the NMR‐based structural elucidation of a series of marine sulfated poly/oligosaccharides discovered in our laboratory within the last 2 years. This set of structures includes the α‐glucan extracted from the bivalve Marcia hiantina; the two sulfated galactans extracted from the red alga Botryocladia occidentalis; the fucosylated chondroitin sulfate isolated from the sea cucumber Pentacta pygmaea; the oligosaccharides produced from the fucosylated chondroitin sulfates from this sea cucumber species and from another species, Holothuria floridana; and the sulfated fucan from this later species. Specific 1H and 13C chemical shifts, generated by various 1D and 2D homonuclear and heteronuclear NMR spectra, are exploited as the primary source of information in the structural elucidation of these marine glycans.

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