A 2023 study showed that scientists can image individual glycan-decorated molecules with low-temperature scanning tunnelling microscopy (STM). The team first electrosprayed intact ions and gently soft-landed them on a surface, then used cryogenic STM to resolve features from the glycans and their protein or lipid partners. The images included glycopeptides, glycolipids, the N-glycoprotein RNase B and an engineered MUC1 reporter fragment.
This is a laboratory demonstration, not a clinical test. Its importance is that it observes glycan placement molecule by molecule rather than reporting only an average over a large population of molecules.
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What the study achieved
Glycans are sugar chains attached to proteins and lipids. Their composition, branching and attachment sites can alter folding, stability, cell recognition and signalling. A sample can contain many closely related glycoforms: molecules with the same protein backbone but different sugars or different occupancy at available attachment sites.
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The paper, “Direct observation of glycans bonded to proteins and lipids at single molecule level,” reports a way to inspect those differences directly. The authors combined soft-landing electrospray ion-beam deposition with low-temperature STM. Instead of analysing a bulk solution and calculating an average structure, they deposited intact glycoconjugate ions on a solid surface and examined individual molecules.
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The approach resolved examples from four broad classes:
- Glycopeptides, in which a short peptide carries one or more glycans.
- Glycolipids, including the gangliosides GM3 and GD3.
- N-glycoproteins, including RNase B.
- An O-glycosylated MUC1 reporter fragment.
Features attributed to individual monosaccharide units were interpreted using shape details such as stereoconfiguration and side groups. Density functional theory (DFT) calculations were used to check whether the proposed molecular arrangements were consistent with the observed images.
Why single-molecule glycan imaging matters
Many glycan measurements are ensemble measurements: thousands or millions of molecules contribute to one signal. Such methods can provide valuable composition or abundance information, but an average can hide the combinations that exist on any one molecule. Two proteins may have the same average number of sugars while carrying them at different sites, or a minority glycoform may be biologically important even when it contributes little to the overall signal.
The authors presented STM as a way to address that specific limitation. It can show where a glycan is attached on a particular molecule and can reveal molecule-to-molecule variation. That does not make ensemble methods obsolete, nor does it prove that STM is more useful for every glycan question. It adds a different type of evidence: a physical image of an individual deposited molecule.
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How the imaging workflow works
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Intact ions are produced by electrospray
The sample is converted into charged droplets and then ions in the gas phase. The goal is to transfer the glycopeptide, glycolipid or glycoprotein without chemically cutting off its attached sugars. Preserving the intact glycoconjugate is essential because the experiment is meant to show the relationship between the glycan and its molecular host.
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The ions are soft-landed on a surface
An ion beam deposits the molecules gently enough that they remain on the surface rather than being shattered on impact. This creates a population of separated molecules that can be located with the STM tip. Surface choice is part of the chemical preparation, not merely a mechanical support.
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The surface is examined at cryogenic temperature
Low-temperature STM scans a sharp conductive tip over the deposited molecules while monitoring tunnelling current. The resulting map contains submolecular features. Cooling helps limit movement and preserves arrangements that would be difficult to resolve if the molecules were mobile during scanning.
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Image features are checked against calculations
DFT calculations provide theoretical structures and electronic information for candidate arrangements. Agreement between calculated and observed features supports the assignment of particular glycan components, while keeping the interpretation tied to a physical model rather than to image appearance alone.
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Why the surface changed for sulfated molecules
Sulfate groups can be chemically labile. For sulfated samples, the team used a more inert silver surface to help preserve those groups. Other samples were imaged on copper. The choice illustrates a practical constraint: the substrate must support imaging while avoiding reactions that alter the glycoconjugate before measurement.
| Surface | Use described in the study | Reason |
|---|---|---|
| Silver | Sulfated molecules | More inert conditions help preserve labile sulfate groups. |
| Copper | Other deposited samples | Used as the imaging substrate for examples not requiring the more inert silver surface. |
What the images revealed
Glycopeptides and glycolipids
The initial demonstrations covered small glycoconjugates, allowing the team to test whether individual sugar features could be distinguished. The reported examples included a glycopeptide derivative and the gangliosides GM3 and GD3. Gangliosides are glycolipids with a ceramide lipid portion and a carbohydrate headgroup; seeing them in the same general workflow showed that the method was not limited to proteins.
The authors reported that image features could distinguish component monosaccharides through details related to stereochemistry and side groups. This is a structural claim about the molecules examined under the instrument conditions, not a promise that every possible sugar in every sample will be identified automatically from a raw STM image.
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1Clear out junk files and repair common Windows errors2Fix the driver behind crashes, sound loss and screen glitches3Repair Windows errors before they cause bigger problemsRNase B: locating one N-glycan at a known site
RNase B is an N-glycoprotein with a well-established glycosylation site. The team imaged individual RNase B molecules and analysed 33 separate N-glycoproteins. The glycan attachment was placed at residue 34 ± 2, matching the known Asn34 attachment site.
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The value of this result is the molecule-by-molecule agreement. Rather than inferring the site only from a population-level measurement, the images placed the attached glycan near the same region on each analysed protein. The “± 2” describes the reported positional spread in this analysis; it is not a general spatial-accuracy specification for all proteins or all STM experiments.
MUC1: variable O-glycan occupancy in an engineered reporter
The MUC1 example used a designed reporter fragment containing 34 potential O-glycosylation sites. Reported images included glycoforms carrying 27, 21 and 20 O-glycans. Across the construct, the paper reported an average of 3.4 O-glycans per tandem repeat and showed that individual sites were occupied to different extents.
These observations demonstrate heterogeneity within the reporter construct. They should not be read as a survey of all human MUC1 in tumors, blood or normal tissue. Native MUC1 varies with cell type and biological state, while the imaged fragment was engineered for the experiment. Chemistry World discussed the possible relevance of MUC1 glycosylation to cancer-biomarker work, but this STM method has not been validated as a cancer diagnostic.
| Sample or construct | Reported observation | How to interpret it |
|---|---|---|
| RNase B | 33 individual N-glycoproteins; attachment at residue 34 ± 2 | Consistent with the known Asn34 site in the molecules analysed. |
| MUC1 reporter fragment | 34 potential O-glycosylation sites; examples with 27, 21 and 20 O-glycans | Shows variable occupancy in an engineered construct. |
| MUC1 reporter fragment | Average of 3.4 O-glycans per tandem repeat | Construct-specific average, not a value for all native MUC1. |
| Gangliosides | GM3 and GD3 examples | Demonstrates imaging of lipid-bound glycans as well as protein-bound glycans. |
What this method can and cannot establish
What it can add
- Direct visual evidence that a glycan is attached to a particular molecule.
- Information about attachment position at the scale resolved by the experiment.
- Observation of different glycoforms and site occupancy from molecule to molecule.
- Structural clues for individual sugar units, supported by DFT modelling.
- A common imaging strategy for selected glycopeptides, glycolipids, N-glycoproteins and O-glycoproteins.
What it does not show
- It does not image glycans inside living cells or observe glycosylation as it occurs in real time.
- It does not establish a clinical assay, diagnostic threshold or patient outcome.
- It does not provide a validated throughput, sensitivity or cost advantage over other analytical methods.
- It does not mean every molecule in a complex biological sample will land in an imageable orientation.
- It does not turn the MUC1 reporter results into a statement about all human MUC1.
How it differs from bulk glycan analysis
The study did not report a head-to-head performance comparison with other analytical techniques, so numerical rankings would be unjustified. The distinction is best understood by asking what each measurement represents.
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| Question | Low-temperature STM after soft landing | Ensemble-oriented methods |
|---|---|---|
| Unit of observation | Individual deposited molecules | Signals averaged across many molecules or fractions |
| Site information | Can show the location of an attached glycan on an imaged molecule | May infer sites from combined chemical, enzymatic or spectrometric evidence |
| Sample state | Intact ions transferred from solution to a solid surface | Depends on the technique; may involve intact samples, fragments or separated populations |
| Preparation demands | Electrospray, controlled soft landing, conductive substrate and cryogenic STM | Technique-specific preparation and instrumentation |
| Output | Submolecular topographic/electronic images interpreted with calculations | Often spectra, chromatograms or aggregate structural measurements |
| Throughput and clinical utility | Not established by this demonstration | Not comparable without a defined method and study design |
In practice, the imaging approach is most naturally viewed as complementary evidence. A bulk method can survey composition across a sample, while STM can test whether a proposed attachment pattern is actually present on individual deposited molecules. The balance between those approaches will depend on sample complexity, the number of molecules needed and the structural question being asked.
Practical constraints for laboratories
This is a specialist workflow rather than a benchtop test. A laboratory would need an electrospray source capable of transmitting intact glycoconjugate ions, an ion-transport and soft-landing arrangement, suitable metal substrates, a cryogenic STM and expertise in interpreting submolecular images. Sulfated compounds may require especially careful surface selection to avoid losing their sulfate groups.
Sample preparation also affects what can be concluded. The molecules must survive transfer from solution into the gas phase and then deposition onto a surface. Orientation, surface interactions and the number of molecules that can be found and imaged all influence the final dataset. The paper demonstrates feasibility for selected samples; it does not specify a routine protocol for every glycoprotein or a universal preparation yield.
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Not on the evidence reported here. The study establishes a physical imaging method and shows biologically interesting examples, including MUC1-related glycosylation. It does not test patient specimens, classify disease states, measure diagnostic sensitivity or specificity, or compare results with an approved clinical assay.
The authors have indicated that further development could help identify unknown glycoproteins and glycolipids. That is a prospective direction, not a demonstrated clinical capability. Before the method could support diagnosis, laboratories would need validated sample handling, reproducible identification criteria, controls, appropriate throughput and evidence that the observed glycoforms correlate with a clinically meaningful condition.
Publication details
The paper appeared in Science, volume 382, issue 6667, pages 219–223, dated 12 October 2023. Its DOI is 10.1126/science.adh3856. The author list includes Kelvin Anggara, Laura Sršan, Thapakorn Jaroentomeechai, Xu Wu, Stephan Rauschenbach, Yoshiki Narimatsu, Henrik Clausen, Thomas Ziegler, Rebecca L. Miller and Klaus Kern.
The central claim is deliberately specific: individual glycoconjugate molecules can be analysed by direct imaging with low-temperature STM after intact ions are deposited by soft landing. The RNase B and MUC1 examples show why that perspective is useful, while the laboratory setup and construct-specific samples define the limits of what has been demonstrated.
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