New tool helps researchers better understand protein interactions
Oeiras, 11th April 2025
Molecules within cells, such as proteins and DNA, are constantly interacting and assembling in complex ways to control everything that happens in living organisms. Learning about these interactions is crucial to understand how our bodies function, how diseases develop, and how we can develop better treatments.
Existing methods such as Small-Angle X-ray Scattering (SAXS) and Isothermal Titration Calorimetry (ITC) are widely used to study molecular interactions. However, they have limitations. ITC, while effective in measuring how tightly molecules bind to each other, something called the dissociation constant (KD), does not provide detailed structural information. On the other hand, SAXS provides structural information but struggles with biological systems that rapidly change or involve multiple interacting molecules.
Now, researchers developed KDSAXS, a new computational tool that improves upon SAXS. This tool takes both experimental SAXS data and theoretical models that describe molecular behavior. This allows KDSAXS to estimate how tightly molecules bind to each other (KD) more accurately, even in complicated systems involving multiple interacting species. "By analyzing how proteins scatter X-rays under different conditions, such as varying concentrations and temperatures, it provides a clearer picture of molecular interactions, their changes over time, and their binding strength," explains Tiago Gomes, first author of the study and a postdoc at ITQB NOVA.
The team tested and validated this new tool using a milk protein, β-lactoglobulin (BLG), that changes its structure depending on conditions like pH, and the interaction between PCNA and p15PAF, a complex involved in DNA repair. In both cases, the method provided accurate KD values and more detailed insights into how these molecules interact, showing its potential to analyze complex biological processes. The study is published in the Journal of Molecular Biology.
“KDSAXS allows researchers to study protein-protein interactions, drug-binding events, and disease-related molecular mechanisms with much greater precision than previous methods”, explains Tiago Cordeiro, head of the Dynamic Structural Biology laboratory who led the study. This open-source tool (https://kdsaxs.itqb.unl.pt/), available on GitHub, is user-friendly and requires minimal computational expertise, making it accessible to researchers across various fields.
This study was developed in collaboration with the Molecular Simulation laboratory, led by António Baptista, the Barcelona Institute of Science and Technology and ICREA, in Spain, and the Centre de Biologie Structurale, Université de Montpellier, in France.
ITQB NOVA researchers (from the left to the right) Tiago Cordeiro, Tiago Gomes and António Baptista.
