Understanding the shape of proteins is important in biology and medicine. Proteins help in building body tissues, supporting cell functions, and fighting diseases. To study proteins more deeply, scientists use a special method called crystallography. This method lets researchers see the tiny parts inside proteins and discover how they work. At the University of Oxford, researchers like Yishun Lu are making big changes in how scientists use crystallography. His work with long-wavelength crystallography helps improve the quality of images and unlocks new possibilities for medicine and structural biology.
Table of Contents
Protein and Its Importance
- Protein Functions
Proteins play key roles in the body, such as building tissues, repairing cells, and regulating body processes. - Protein Sources
- Meat
- Eggs
- Milk
- Fish
- Beans
- Protein Role in Health
- Helps the body grow and stay strong
- Supports the immune system
- Aids in creating medicines by revealing cell behaviours
What is Crystallography?
Crystallography is a method that shows the inner structure of proteins by turning them into crystals. These crystals allow scientists to see protein shapes using X-rays.
Steps in Crystallising Proteins
- Evaporation – Slowly drying a protein solution forms crystals.
- Chemical Addition – Mixing proteins with specific chemicals causes crystals to grow.
- Temperature or pH Change – Adjusting the temperature or pH of the solution promotes crystallisation.
Once proteins are crystallised, X-rays pass through them, producing images that reveal their structure. These images are used to learn how proteins behave and how they can be targeted for treatment.
Long-Wavelength Crystallography
Long-wavelength crystallography helps scientists see certain parts of proteins more clearly. However, this method faces one big problem: absorption errors.
Issue with Absorption
- In standard X-ray diffraction, Absorption effects are small.
- In long-wavelength diffraction, Absorption causes major errors that reduce data quality.
Solution by Yishun Lu
Yishun Lu, a final-year DPhil student at Oxford’s Department of Engineering Science, works with Beamline I23 at Diamond Light Source. His research focuses on correcting absorption errors in long-wavelength crystallography.
Key Contributions
| Method | Details |
|---|---|
| Ray Tracing | Follows X-rays through the crystal to track how they bend or scatter. |
| Tomography Reconstruction | Creates a 3D model of the sample to improve the accuracy of measurements. |
| GPU Acceleration | Uses Graphics Processing Units to speed up computations. |
| Software Used | AnACor 2.0 – Faster and more accurate than the earlier version. |
Ray-Tracing Technique
- Simulates the path of X-rays as they hit and pass through crystals.
- Determines how much X-rays are absorbed at each point.
- Identifies material types such as:
- Crystal
- Sample mount
- Mother liquor
- Oils or glue
Advantages of Ray Tracing
| Feature | Benefit |
|---|---|
| Accurate Path Tracking | Finds precise X-ray paths through different materials. |
| 3D Modelling | Builds exact models of the samples using tomography. |
| Noise Removal | Cleans up unwanted signals using image processing. |
| Improved Computation | Runs 180 times faster than earlier software versions. |
| Better Absorption Correction | Results in clearer, more accurate protein images. |
AnACor 2.0 Software
- Combines ray tracing with image processing.
- Performs faster corrections.
- Gives accurate structural data.
- Open-source and designed for crystallographers.
Impact on Structural Biology and Drug Design
Accurate images of proteins help scientists understand how diseases work. This leads to:
- Precise Atom Location
- Detailed Protein Modelling
- Improvement in AI Tools like AlphaFold3
- Faster Drug Development
Breakthrough Applications
| Application Area | Impact |
|---|---|
| Structural Biology | Clearer protein structures help understand biological systems. |
| Drug Design | Accurate images allow scientists to target proteins with better medicines. |
| Artificial Intelligence | Tools like AlphaFold3 benefit from higher-quality data. |
| Medical Research | Discoveries lead to faster, safer, and more effective treatments. |
Research Team and Collaboration
- Yishun Lu – Final-year DPhil student, Oxford e-Research Centre
- Supervisor – Professor Wes Armour
- Partner – Beamline I23, Diamond Light Source
- Focus – Ray tracing, GPU computing, absorption correction, image processing
Published Research
| Title | Journal |
|---|---|
| Ray-tracing analytical absorption correction for X-ray crystallography | Journal of Applied Crystallography 57.3 (2024) |
| AnACor2.0: GPU-accelerated software for absorption correction | Journal of Applied Crystallography 57.6 (2024) |
Visual Example
A yellow loop is used in the setup to hold the protein crystal. This loop removes the crystal from the solution and places it under the X-ray beam. X-rays are then passed through the crystal, and the ray-tracing method maps the path of these X-rays to study how they interact with the material.
Example of Real-World Use
- SARS-CoV-2 Protein Crystals – These crystals help researchers understand how the virus spreads.
- Medical Treatments – Crystal structures of proteins guide scientists in developing vaccines and treatments.
Moving Forward
Crystallography gives scientists the power to see inside proteins. With new methods like ray tracing and faster software like AnACor 2.0, researchers at the University of Oxford are improving long-wavelength crystallography. This breakthrough improves data quality, speeds up research, and supports progress in drug development and biotechnology. Seeing proteins clearly at the atomic level brings us closer to solving health problems and developing better medicines.
