Dynamics in liquid-ligand-proteins systems

This project is based on the integration of knowledge from biology, chemistry, and physics. It focuses on advancing understanding of how the physical properties of liquids influence the behavior of ligand molecules — small particles that form the basis of many medicines and can bind to proteins in the body. Special attention is given to how these molecules behave both in solutions and directly inside the "pockets" of proteins — small “niches” where important processes affecting cell function occur. The primary objective is to determine how external factors, such as the composition of the surrounding liquid or temperature (especially within the range close to human body temperature), affect the movement and interactions of these molecules with their liquid environment. Furthermore, the study seeks to clarify how these molecules interact with proteins and how these interactions relate to changes in the structure and behavior of solutions in such systems. Modern computational techniques — molecular modeling — are employed, enabling visualization of the movement and interaction of individual molecules, akin to a slow-motion movie. Additionally, physics methods traditionally used to study liquids and solutions are adapted and improved to better understand the complex biological systems involving liquids, ligands, and proteins. The project’s main innovation lies in revealing how molecules “dock” with proteins at the smallest scale — literally from the inside. Various computational models are compared to identify which best represent real processes. This is crucial because precise knowledge of the number of water molecules surrounding a drug molecule in a protein pocket significantly aids the interpretation of experimental data. Ultimately, the results contribute not only to a deeper understanding of fundamental molecular interactions but also to the development of new ideas for experimental research. Importantly, these insights support the creation of new medicines. Given the ongoing quest in modern medicine for effective and safe drugs, understanding molecular interactions at a fundamental level can substantially accelerate this process and reduce associated costs.