Multi-scale simulations of galectin-3

Intrinsically disordered proteins (IDPs) at physiological conditions have no well-defined, stable structure in extended parts of their polypeptide chains. They participate in many processes in biological cells, including signaling, cell-cycle regulation, and initiation of translation.

IDPs are major components of biomolecular condensates (BCs) that form through liquid-liquid phase separation in biological cells. Despite considerable research on BCs in the cytosol and nucleus, their behavior at cellular membranes remains largely unexplored.

Galectin-3 is a protein comprising an intrinsically disordered N-terminal domain (NTD) and a well-folded carbohydrate recognition domain (CRD) which can bind to glycosphingolipids on the cell membrane. Galectin-3 is known to mediate clathrin-independent endocytosis [1] and has been recently shown to undergo liquid-liquid phase separation [2], but the function of the BCs of galectin-3 in the endocytic pit formation is unknown.

Using dissipative particle dynamics (DPD) simulations, we explore how polymer models resembling galectin-3 sense and respond to membrane curvature. Our findings suggest a generic mechanism by which BCs sense membrane curvature, potentially influencing such cellular processes as endocytosis [3]. To elucidate the conformational dynamics of galectin-3, we have conducted molecular dynamics simulations using the Martini 3 force field. Following the method introduced by Thomasen et al. [4] for rescaling protein-water interactions, we generate a conformational ensemble in good quantitative agreement with data from small angle X-ray scattering experiments [5]. Our simulations reveal large-scale fluctuations between compact and extended conformations of galectin-3, with aromatic residues within the NTD forming most frequent contacts [6].

[1] Ramya Lakshminarayan, Christian Wunder, Ulrike Becken, Mark T. Howes, Carola Benzing, Senthil Arumugam, Susanne Sales, Nicholas Ariotti, Valérie Chambon, Christophe Lamaze, Damarys Loew, Andrej Shevchenko, Katharina Gaus, Robert G. Parton & Ludger Johannes, Galectin-3 drives glycosphingolipid-dependent biogenesis of clathrin-independent carriers, Nature Cell Biology 16, 592-603 (2014)

[2] Yi-Ping Chiu, Yung-Chen Sun, De-Chen Qiu, Yu-Hao Lin, Yin-Quan Chen, Jean-Cheng Kuo & Jie-rong Huang, Liquid-liquid phase separation and extracellular multivalent interactions in the tale of galectin-3, Nature Communications11, 1229 (2020)

[3] Midhun Mohan Anila,a Rikhia Ghoshb and Bartosz Różycki, Membrane curvature sensing by model biomolecular condensates, Soft Matter 19, 3723-3732 (2023)

[4] F. Emil Thomasen, Francesco Pesce, Mette Ahrensback Roesgaard, Giulio Tesei, and Kresten Lindorff-Larsen, Improving Martini 3 for disordered and multidomain proteins, Journal of Chemical Theory and Computation 18, 2033-2041 (2022)

[5] Yu-Hao Lin, De-Chen Qiu, Wen-Han Chang, Yi-Qi Yeh, U-Ser Jeng, Fu-Tong Liu, and Jie-rong Huang,The intrinsically disordered N-terminal domain of galectin-3 dynamically mediates multisite self-association of the protein through fuzzy interactions, Journal of Biological Chemistry, 292, 17845-17856 (2017)

[6] Anila, M. M., Rogowski P., & Różycki, B., Scrutinising the conformational ensemble of the intrinsically mixed-folded protein galectin-3 Under review. (2024)