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Crystal based Glycoprotein & Carbohydrate Binding Analysis Service

High-Resolution Structural Insights to Accelerate Your Glycoprotein Research

Are you currently facing difficulties resolving complex protein-glycan structures, decoding multivalent avidity, or mitigating the high thermodynamic cost of drug binding? Our specialized Glycan Crystal & Glycoprotein Crystal Analysis Services help you transform unknown biomarkers into actionable drug targets through advanced X-ray co-crystallography and computational structural biology focused exclusively on resolving native-like glycan binding structures. Our analysis service helps you validate targets and de-risk leads by providing the definitive structural and biophysical basis of function.

Monoglucosylated N-glycan on Antheraea pernyi arylphorin. (OA Literature)Fig.1 Crystal structure of the Antheraea pernyi arylphorin (APA) and its glycans.1

Discover How We Can Help

Glycosylation is the most common post-translational modification, dictating protein function, immune response, and folding. However, the inherent mobility and chemical heterogeneity of sugar chains have historically limited structural resolution (with only a small fraction of solved structures capturing defined N-glycans). Creative Biolabs' service directly addresses this structural bottleneck by specializing in co-crystallography of glycoproteins with their ligands, providing the atomic-level detail necessary. Our service is specifically engineered to address the critical gaps in structural glycobiology that frustrate drug development. We provide the high-resolution evidence required to validate binding mechanisms, enabling the rational design of small molecules or biologics targeting glycan interfaces.

Key Step Activities Involved Expected Outcomes
Sample Assessment Initial screening of client-provided protein viability and glycosylation profile. A customized work plan and protocol defining protein-to-glycan ratios, expression system choice, and crystallization strategy.
Homogeneous Glycoprotein Production Utilizing specialized cell lines or enzymatic modification to generate a single, uniform glycoform of the target protein. This overcomes glycan heterogeneity, which hinders crystallization. Highly pure target glycoprotein with a defined, uniform N-glycan structure suitable for crystallization.
Co-Crystallization and Optimization Extensive high-throughput screening of crystallization conditions for the target alone and in complex with various carbohydrate ligands. Well-diffracting crystals of the glycoprotein-ligand complex are ready for analysis.
Data Collection Collect high-flux X-ray data. Phase determination, detailed model building, and rigorous validation checks are performed using advanced software. A robust, validated 3D model with clear electron density for the bound carbohydrate ligand and neighboring amino acid residues.
Mechanistic Interpretation & Reporting Analysis of protein-carbohydrate interactions (hydrogen bonds, aromatic stacking forces), active site confirmation, and comparison to known structural homologs. Comprehensive final report detailing binding mode, affinity predictions, and strategic recommendations for downstream drug design.

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Professional knowledge and project experience

We possess over 20 years of experience characterizing glycoproteins and carbohydrates, focusing on their unique binding mechanisms.

Overcoming glycan flexibility

Our protocols specifically minimize glycan disorder, a major obstacle where glycan electron density is typically lost. We leverage specialized cryo-protectants and crystallization matrices to capture the ordered, functional conformation required for drug targeting.

Service Features

Validated glycoform homogeneity

Unlike general structural labs, we integrate proprietary enzymatic and cell-line techniques to ensure the target protein possesses a homogeneous N-glycan structure, dramatically increasing the success rate of complex crystallization.

High-resolution ligand mapping

We reliably map subtle binding differences, such as the preference of certain sugar chain lengths for the central subsite versus the distal subsites, providing atomic-level detail for lead optimization.

The importance and application of this service are profound:

  • Rational drug design: Resolving the hydrogen bonds and hydrophobic stacking of aromatic residues that define the binding groove provides the precise coordinates needed for medicinal chemistry to design potent, non-carbohydrate small molecule mimetics.
  • Target validation and mechanism of action: For high-value biomarkers, structural clarity transforms clinical association into a verifiable mechanism of action.
  • Biologic optimization: For antibody therapeutics, confirming the structural role of the Fc N-glycan is vital for understanding and modulating effector functions.

Published Data

The study focuses on the human cartilage glycoprotein-39 (HCgp-39), a protein frequently found at elevated levels in patients suffering from rheumatoid arthritis and certain cancers, though its precise purpose remains a mystery. Researchers determined its detailed 3D structure using X-ray crystallography, revealing a large, barrel-shaped core structure typically associated with enzymes that break down chitin. However, HCgp-39 is unique because, despite binding to chitin, it lacks this destructive enzymatic activity and instead functions as a lectin, or a sugar-binding protein.

The analysis unveiled a prominent, long groove on the protein's surface, which acts as the binding site for carbohydrates. Through soaking the protein crystals with various chitin fragments, the team mapped out nine distinct sugar-holding positions, or subsites, within this groove. Crucially, the complex structures, which are visually detailed in the Figure, showed that HCgp-39's affinity is highly dependent on the size of the sugar chain. The study found a remarkable size-dependent binding pattern: short chitin molecules (like disaccharides) preferentially anchor themselves at the more open, distant ends of the groove. Conversely, longer chains (four or five units long) strongly favor the central, deeper positions. When these longer chains bind centrally, the protein forces the sugar into a strained, non-linear shape, a conformation typically seen only when a sugar is about to be broken down by an active enzyme. This unique dual-binding mechanism, never before seen in similar proteins, suggests HCgp-39 may be involved in complex signaling, perhaps by recognizing structures similar to chitin, such as those found on the beginnings of hyaluronic acid chains, which are important in tissue healing and inflammation.

Characterization results of human cartilage glycoprotein-39 and chitin conjugates. (OA Literature)Fig.2 Structure of HCgp-39 in complex with chitin.2

FAQs

We have a highly flexible glycoprotein. Can crystallization provide useful data if the glycan is disordered?

Yes, absolutely. While crystallography may not resolve the entire glycan, it often provides atomic resolution for the critical chitobiose core and the neighboring residues that anchor the glycan. Crucially, our service then utilizes molecular dynamics simulation to model the function of the disordered, flexible portions and calculate their true impact on ligand access and binding energy.

What information do I need to provide if my target is a complex N-glycan from a viral envelope?

We primarily require the purified glycoprotein (if available) and the target sequence to engineer the correct homogenous glycoform in our specialized expression systems. If the specific glycan is known (e.g., Man-9), providing a highly purified sample of that oligosaccharide is ideal for complex formation and cocrystallization.

My target lectin is highly flexible; how can you ensure the carbohydrate will be visible in the electron density?

Our strength lies in stabilizing the complex. We utilize specialized crystallization chaperones, test a diverse range of ligand concentrations to achieve high occupancy, and employ advanced refinement techniques to meticulously model even partially ordered glycan atoms. We focus on capturing the functional, bound conformation.

Customer Review

Unmatched Detail
"Using Creative Biolabs' crystal based glycoprotein & carbohydrate binding analysis service in our research has significantly improved the confidence in our lead molecule selection by resolving the bisecting N-acetylglucosamine interaction site on our cell-surface receptor. Their high-resolution structure was instrumental."- Ja***on, Scientist.

Target Validation Speed
"The ability of Creative Biolabs to produce and crystallize a core Man5GlcNAc2 glycoform of our secreted protein was a game-changer. It facilitated functional validation and shaved months off our initial structural timeline compared to our in-house attempts with heterogeneous material."- E***a, Scientist.

Challenging Lectin Solved
"Creative Biolabs' structural analysis of our chitinase-like protein immediately explained the observed length-dependent ligand affinity. This was a critical insight, moving us from general carbohydrate screening to targeted synthesis of specific sugar mimetics."- A***a, Project leader.

Extended Services

Custom glycoprotein production service

For clients requiring a guaranteed supply of highly homogeneous, correctly folded glycoproteins for downstream assays.

Binding kinetics and affinity analysis

Utilizing Surface Plasmon Resonance (SPR) and Isothermal Titration Calorimetry (ITC) to quantify the affinity and thermodynamic parameters of the carbohydrate-protein interaction before crystallography.

Glycoprotein analysis

Detailed mass spectrometry analysis of N-glycan structures on therapeutic antibodies (e.g., IgG), essential for optimizing effector functions. In addition, we also provide various Glycoprotein Crystal Analysis Services, including Crystal Structural Analysis, Glycosylation Site Analysis, and Glycosylation Type Analysis services.

How to Contact Us

Creative Biolabs is your trusted partner for resolving the most complex challenges in structural glycobiology. We transform structural ambiguity into actionable, high-resolution insights, enabling the rational design of next-generation anti-inflammatory and anti-cancer therapeutics targeting critical lectin pathways. Creative Biolabs is a structural glycobiology specialist. We provide the precision and insight required to navigate the challenging field of protein-carbohydrate crystallography, which has a low success rate. To initiate your project or discuss your specific structural challenge, please reach out to our team directly.

References

  1. Nagae, Masamichi, and Yoshiki Yamaguchi. "Function and 3D structure of the N-glycans on glycoproteins." International journal of molecular sciences 13.7 (2012): 8398-8429. Distributed under an Open Access license CC BY 3.0, without modification. https://doi.org/10.3390/ijms13078398
  2. Fusetti, Fabrizia, et al. "Crystal structure and carbohydrate-binding properties of the human cartilage glycoprotein-39." Journal of Biological Chemistry 278.39 (2003): 37753-37760. Distributed under an Open Access license CC BY 4.0, without modification. https://doi.org/10.1074/jbc.M303137200
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