Biology subjects

Perez-Segura, C.

Publications and source records attributed to Perez-Segura, C..

4 recordsLinked to original sources

bioRxiv2026

Toward Robust Characterization of Dynamic Binding Pockets: Lessons from the HBV Capsid Assembly Modulator Site

Protein function often depends on ligand binding pockets that fluctuate among conformational states, altering their size, shape, topology, and accessibility, yet quantitative comparison of these dynamic cavities remains challenging because their boundaries are often inherently ambiguous. The measure volinterior algorithm uses fuzzy-boundary detection to characterize enclosed molecular spaces; here, the hepatitis B virus (HBV) capsid assembly modulator (CAM) binding site is used as a model system to develop and validate a practical workflow for applying the method to dynamic protein binding pockets. The resulting methodology provides practical guidance for parameter selection and evaluation, establishes a standardized protocol for quantitative characterization of the HBV CAM pocket, and demonstrates robust, reproducible performance across conformational ensembles derived from molecular dynamics (MD) simulations. More broadly, this work provides a reproducible strategy for adapting measure volinterior to other dynamic binding pockets, enabling consistent comparison of pocket geometry among independent structural studies. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=105 SRC="FIGDIR/small/743403v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@540692org.highwire.dtl.DTLVardef@7b94dborg.highwire.dtl.DTLVardef@169c478org.highwire.dtl.DTLVardef@e1de80_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2026

Modeling Reveals How Direct-Acting Antivirals Redirect HBV Capsid Assembly Pathways to Noninfectious Products

Hepatitis B virus (HBV) infections cause chronic liver disease, resulting in about one million deaths per year, and there is currently no cure. Recent work has shown that a class of small molecules called capsid assembly modulators (CAMs) is promising for treating HBV. CAMs bind to HBV capsid protein subunits and alter their assembly, leading to non-functional and malformed structures rather than functional, closed shells. However, the mechanisms by which CAMs alter capsid assembly pathways remain unclear. Here, we extend a recently-developed kinetic Monte Carlo (KMC) model for HBV capsid assembly to simulate how CAMs affect assembly. In the model, CAMs alter assembly by preferentially binding to interfaces between certain quasi-equivalent subunit conformations. Simulations of the model reproduce experimental assembly product distributions. By analyzing assembly trajectories, we clarify the roles of thermodynamics and kinetics in determining assembly products, identify assembly mechanisms, and predict the key intermediates that lead to either capsids or malformed structures. Our findings enhance our fundamental understanding of capsid assembly, help advance the development of CAMs as a treatment for HBV and, more broadly, inform efforts to direct self-assembly pathways toward specific products.

biophysics↗

bioRxiv2026

Assembly-active and -inactive forms of HBV capsid protein provide distinctly different binding sites for capsid assembly modulators

In an infection, Hepatitis B Virus (HBV) core protein (HBc) normally assembles into icosahedral capsids. Capsid Assembly Modulators (CAMs) are direct acting antivirals that induce HBc mis-assembly and are the subject of active research and development. Two versions of HBc are used in structural studies of CAM-HBc complexes: Cp150 and Cp149-Y132A. Cp150 forms empty icosahedral capsids that are structurally indistinguishable from those found in virions. The Y132A mutation of Cp149 leads to an assembly defective soluble protein that crystalizes as flat hexagonal sheets, where the hexagons resemble icosahedral quasi-sixfold vertices. In this study, we compare structures of CAM-bound Cp150 to CAM-bound Cp149-Y132A. In capsids, the residues forming the CAM site shift to match the structure of bound CAMs, an induced fit. In Cp149-Y132A crystals, CAM sites show little structural adjustment in response to different CAMs binding. In turn, the array of residues that interact with CAMs varies from CAM to CAM in capsid structures but remains nearly constant in Cp149-Y132A crystals. These results illustrate important differences between CAM binding in Cp149-Y132A and Cp150 structures that will contribute to future CAM design.

biochemistry↗

bioRxiv2025

Mechanistic insights into CAM-induced disruption of HBV capsids revealed by all-atom MD simulations

Capsid assembly modulators (CAMs) represent a promising antiviral strategy against hepatitis B virus (HBV), but their effects on preformed capsids remain incompletely understood. Here, all-atom molecular dynamics (MD) simulations of intact HBV capsids complexed with prototypical CAM-As (HAP1, HAP18) and CAM-Es (AT130), reveal how structural changes induced by small molecule binding in the interdimer interfaces propagate through the shell lattice to yield global morphological consequences. Each quasi-equivalent interface exhibits a unique response: A sites, located within the pentameric capsomers, are unfilled in these systems and altered marginally by the presence of CAMs in neighboring interfaces. B sites are the most open and "CAM-ready," suggesting uptake requires minimal conformational perturbation on the local or global level. C sites emerge as hubs of allosteric control and the key drug target, as their occupancy creates local distortion that is broadcast to adjacent sites, driving capsid faceting and - in the case of CAM-As - the destabilization that precedes dissociation in favor of aberrant assembly. D sites, unfilled in these systems, act as structural sinks, absorbing distortions from adjacent interfaces within the hexameric capsomers. The extent of C site adjustment and the nature of D site counterbalance varies with CAM chemotype, highlighting the divergent effects of CAM-As versus CAM-Es. The tensegrity relationship between the four quasi-equivalent interfaces couples them into a global network for strain redistribution that is functionally allosteric, with CAM binding sites displaying signs of both positive and negative cooperativity. These new insights into HBV capsid dynamics clarify how CAMs alter them on the microsecond timescale and suggest that targeting strain redistribution in mature core particles could be leveraged therapeutically. Author summaryHepatitis B is a major cause of chronic liver disease worldwide. The virus relies on a protein shell, called the capsid, to protect and deliver its genetic material to the host cell during infection. Some experimental drug molecules attack this shell, either forcing it to assemble incorrectly or breaking it apart after it has formed. To understand how these molecules work, we used powerful computer simulations to model the capsid at the level of individual atoms. We discovered that when molecules bind the capsid at certain sites, they create strain that spreads across the shell, sometimes leading to large distortions and instability. These insights explain how small molecules can disrupt the virus and point the way toward designing better antiviral therapies.

biophysics↗