Resumen en inglés

ABSTRACT: cells have developed the capability to compartmentalize and generate organelles without membranes, known as membraneless organelles. These organelles take shape through a process called liquid-liquid phase separation (LLPS), resulting in condensed droplets. Membraneless organelles are primarily composed of proteins that lack a well-defined three-dimensional structure, known as intrinsically disordered proteins (IDPs). They can undergo assembly and disassembly in response to changes in the cellular environment. The formation of these organelles is facilitated by weak interactions between proteins, and when protein concentrations are high and temperatures are low, phase separation occurs. DEAD-box helicase 4 (Ddx4) is an essential protein involved in the development of germ cells. Its primary function is to regulate RNA metabolism and interact with other proteins. The formation of Ddx4 aggregates relies on specific electrostatic interactions, and even slight modifications in individual chains can cause the dissolution of the cellular structure under certain physiological circumstances. To observe the physical characteristics of Ddx4 aggregates, researchers often employ biological markers such as fluorescent proteins. One commonly used biomolecule for visualizing cellular structures is the Green fluorescent protein (GFP). The results of experiments have shown that Ddx4 aggregates can selectively absorb or exclude GFPs based on their charge. This behavior is attributed to the interactions between proteins at the molecular level. However, studying these interactions experimentally is challenging due to the small size of the proteins and the short timescales involved. To overcome these limitations and reduce material costs, molecular dynamics (MD) simulations are employed as an alternative approach. In this study, MD simulations are utilized to investigate the interaction between Ddx4 aggregates and GFPs with different molecular charges. This enables a better comprehension of the interactions between membraneless organelles and other biomolecules.