Predicting charge of a nucleosome core particle based on its environment
Predicting charge of a nucleosome core particle based on its environment lead image
Nucleosomes are key to organizing DNA in our cells. Each nucleosome forms when DNA wraps around a core of proteins, and these units link together in a chain resembling beads on a string. The chain is then tightly packed to form chromosomes, ensuring the long string of DNA is efficiently organized and compacted to fit within the nucleus.
The nuclear environment impacts the charge of the nucleosome core particle (NCP), and Szleifer et al. created a theoretical model to predict this charge.
“The effective charge of an NCP emerges from a delicate and complex balance involving the chemical dissociation equilibrium of the amino acids and the DNA phosphates, the electrostatic interaction between them, and the translational entropy of the mobile solution ions,” author Igal Szleifer said.
To their surprise, divalent Mg2+ concentrations had a large effect on NCP charge, which the researchers were able to show was caused by the ion bridging of two DNA-phosphates and one magnesium ion. However, this is not the only factor affecting the charge.
“We demonstrate that to describe and predict the charged state of an NCP properly, it is essential to consider molecular details such as DNA-phosphate ion condensation, and the acid-base equilibrium of the amino acids that comprise the core histone proteins,” Szleifer said.
There are ways to test this theory in vivo using optical imaging techniques.
“Part of our theoretical research is focused on nucleosome level of understanding in chromatin,” Szleifer said. “Given the complex charge system of chromatin and its environment, we aim to understand how the electrostatic interactions of the nuclear electrolyte environment determine the charge and structure of chromatin.”
Source: “The impact of charge regulation and ionic intranuclear environment on the nucleosome core particle,” by Rikkert J. Nap, Paola Carrillo Gonzalez, Aria E. Coraor, Ranya K. A. Virk, Juan J. de Pablo, Vadim Backman, and Igal Szleifer, Journal of Chemical Physics (2024). The article can be accessed at https://doi.org/10.1063/5.0241529 .
This paper is part of the Chromatin Structure and Dynamics: Recent Advancements Collection, learn more here .
