Jul 2026· Current Opinion in Structural Biology· Vol 101, pp.
103345
· 0 citations· 62 references
Medicine
Abstract
Macromolecular crowding is a fundamental feature of the cellular environment that strongly influences biomolecular structure, dynamics, and phase behavior. Despite its significance, it has been a challenge to represent and capture the effects of the crowded environment accurately and sufficiently in molecular simulations. This review discusses the challenges and recent progress in the development of computational approaches for modelling and simulating biomolecular processes in a crowded milieu. The review focuses on the new view of crowding, which highlights the interplay of entropic and enthalpic effects. Emerging data-driven strategies are discussed for improving force-field representations and predicting biomolecular behavior in crowded media, with particular emphasis on generating synthetic datasets, using simulation-derived descriptors, and employing combinatorial frameworks for unravelling microscopic origins of crowding.
This review emphasizes the context-dependent role of crowding in balancing native protein stability against aggregation propensity, highlighting how heterogeneous intracellular environments govern the emergence of functional assemblies or pathological amyloids.
Sanjana Pandey, Neelanjana Sengupta· Current Opinion in Structura...· 0 citations
Cellular membranes are essentially complex and heterogeneous assemblies. The lipid bilayer forms the basis of the membrane architecture, and the associated proteins and surface-exposed glycans, known as glycocalyx, build up a dynamic, highly crowded environment. This intrinsic crowding modulates diffusion within the lipid bilayer, affects the spatial organization of the membrane components, and drives complex membrane morphology. This review addressed several emerging themes, i.e. crowding-induced condensation of intrinsically disordered proteins at the membrane interface and the multifaceted effects of the glycocalyx as a natural crowder at the plasma membrane. We further describe the potential of tailored glycomimetics to enable crowding studies in defined (semi)synthetic systems and molecular sensors as a tool to quantify the dynamics of the membrane-associated crowding.
M. Schmitter, Laura Hartmann, A. Kedrov· Current Opinion in Structura...· 0 citations
Physics-based models of biomolecular systems that explicitly represent biomolecular structure and mechanics, such as atomistic molecular dynamics simulations are well-established because experimental data has been available to iteratively improve and validate models. Now, simulations of the biological mesoscale are growing in importance because of the improvements in experimental tools to visualise this regime. This includes techniques such as cryo-electron microscopy and tomography, microscopies that follow individual proteins in their cellular contexts, in situ scattering to follow the dynamic evolution of biomolecular assembly, and -omics tools. Together, these approaches alone and in combination have revealed the importance of interactomes that bridge multiple scales. Here we describe the theoretical, computational and cultural challenges that need to be overcome to gain an understanding of the biological mesoscale and offer potential solutions. This commentary is the result of a joint CECAM/CCPBioSim discussion workshop on how the community should address the challenges of biomolecular simulations at the mesoscale held in Trento, Italy in the summer of 2024. The aim is to provide a broad overview of the tools and techniques relevant to the biological mesoscale, and to signpost the reader to more detailed discussions within the cited literature.
Sarah Harris, Gianluca Lattanzi, Angelo Rosa et al.· Biophysical Journal· 0 citations
Molecular crowding in cells is not solely a consequence of excluded volume but emerges from interaction networks shaped by RNA and proteins. Here we examine the physicochemical principles underlying RNA-mediated crowding, focusing on how sequence-driven multivalency, structural topology, and network connectivity govern molecular organization. Repeats, secondary structures, and higher-order motifs such as G-quadruplexes act as interaction modules that promote percolation and phase separation, while RNA length and concentration tune phase boundaries. These RNA-encoded features promote multivalent RNA-RNA and RNA-protein interactions that shape condensate assembly, dynamics, and organization across scales. In this framework, crowding emerges as an RNA-centered, interaction-driven property linking molecular features to mesoscale organization in both physiological and pathological contexts.
Jonathan Fiorentino, Michele Monti, Laura Broglia et al.· Current Opinion in Structura...· 0 citations
Biological macromolecules form the cornerstone of cellular architecture and function through diverse structural arrangements and dynamic interactions. Recent methodological breakthroughs have revolutionized our understanding of these complex biomolecular systems by providing unprecedented resolution of their three-dimensional organization and conformational landscapes. This review examines significant advances in both structural elucidation and functional characterization approaches that bridge the critical gap between static snapshots and dynamic behaviors exhibited within cellular environments. Non-cell-based analytical platforms have similarly evolved, offering enhanced sensitivity, multiplexing capabilities, and reduced sample requirements for interrogating molecular interactions under near-physiological conditions. The integration of experimental approaches with computational modeling has enabled the construction of comprehensive structure-function relationships that more accurately represent macromolecular behavior in native contexts. This review aims to provide a contemporary assessment of biological macromolecule research, highlighting how technological advancements continue to fill the existing bridge and integrate the prior understanding of complex biomolecular systems while addressing persistent technical challenges in their characterization, with finesse.
Rabab Fatima, Bhupender Nehra, Biplab Debnath et al.· Critical reviews in analytic...· 0 citations
Complex coacervates are widely used as model systems for studying biomolecular condensate formation, yet how intracellular crowding influences coacervation mechanisms remains unclear. Here, we investigate a model protein–polymer coacervate system in dilute and crowded environments to elucidate its formation mechanism. In dilute solutions, protein–polymer complexes gradually grow into larger assemblies as their net charge approaches neutrality. Under crowded conditions, excluded-volume effects force polymer chains into highly coiled conformations, creating a dense polymer network before the protein is introduced. Protein incorporation into this network relieves conformational tension and triggers the formation of protein–polymer networks that act as scaffolds for coacervates, bypassing the gradual charge-driven assembly seen under dilute conditions. Despite this mechanistic difference, crowders are found to be excluded from the dense phase, yielding comparable mesoscale structures under both conditions. Overall, this work suggests how condensates may adapt their assembly mechanisms within complex cellular environments.
Shanta Biswas, S. Pingali, Katie T. Tran et al.· Biomacromolecules· 0 citations