Work

GRAMMCell: Docking-based Cell Modeling Resource

Year: 2025

Type: article

Abstract: • Environment inside biological cells is highly crowded. • Crowding has a significant impact on protein folding, stability and kinetics. • Computational approaches to cell modeling can provide details of molecular mechanisms. • GRAMMCell web server implements simulations of cell environment at atomic resolution. The environment inside biological cells is densely populated by macromolecules and other cellular components. The crowding has a significant impact on folding and stability of macromolecules, and on kinetics of molecular interactions. Computational approaches to cell modeling, such as molecular dynamics, provide details of macromolecular behavior in concentrated solutions. However, such simulations are either slow, when carried out at atomic resolution, or significantly coarse-grained. Protein docking has been widely used for predicting structures of protein complexes. Systematic docking approaches, such as those based on Fast Fourier Transform (FFT), map the entire intermolecular energy landscape by determining the position and depth of the energy minima. The GRAMMCell web server implements docking-based approach for simulating cell crowded environment by sampling the intermolecular energy landscape generated by GRAMM (Global RAnge Molecular Matching). GRAMM systematically maps the landscape by a spectrum of docking poses corresponding to stable (deep energy minima) and transient (shallow minima) protein interactions. The sampling of these energy landscapes of a large system of proteins is performed in GRAMMCell using highly optimized Markov Chain Monte Carlo protocol. The procedure allows simulation of extra-long trajectories of large, crowded protein systems with atomic resolution accuracy. GRAMMCell is available at https://grammcell.compbio.ku.edu.

Source: Journal of Molecular Biology

DOI: 10.1016/j.jmb.2025.169085