Biology subjects

Khavani, M.

Publications and source records attributed to Khavani, M..

3 recordsLinked to original sources

bioRxiv2026

3D-Printable and Cytocompatible Hydrogel from Acinetobacter baylyi ADP1 Extracellular Matrix

Tissue engineering has advanced significantly, yet multicomponent hydrogels inspired by the compositional complexity of natural extracellular matrices (ECMs) are still underexplored. Most current hydrogels are based on single-component formulations, which can limit their biochemical and mechanical versatility. Developing synthetic multicomponent hydrogels remains challenging because it requires the controlled integration of multiple functional groups within a single material platform. Here, a biologically driven strategy is introduced by leveraging Acinetobacter baylyi ADP1, a bacterium that naturally produces extracellular polymeric substances (EPS) composed of a multicomponent matrix of polysaccharides and proteins. Through three-day cultivation and a simple extraction method, a hydrogel is obtained that can be methacrylated and photocrosslinked using red or blue light. This hydrogel is porous, cytocompatible, 3D-bioprintable, injectable, and undergoes rapid gelation for in situ crosslinking. This work highlights the potential of using bacterial-derived multicomponent hydrogels for biofabrication.

bioengineering↗

bioRxiv2026

Multiscale Free-Energy Methods for Protonation-Coupled Light-Responsive Binding of Ionizable Photoswitchable eDHFR Inhibitors

Photoswitchable ligands enable photocontrol of biomolecular activity by binding to targets in an isomer-dependent, light-responsive manner. Recent developments in ionizable photoswitchable ligands greatly expand their applications but introduce a major design challenge: light-responsive binding can depend on isomeric form, chemical substitution, and binding-induced shifts in protonation equilibria. These effects are tightly coupled, subtle in magnitude, and difficult to predict. Consequently, few computational methods have been developed and systematically benchmarked for quantitatively predicting them. Here, we establish a multiscale free-energy method and benchmark it against experimental data for a series of recently developed photoswitchable inhibitors of Escherichia coli dihydrofolate reductase (eDHFR), a crucial target in photopharmacology. Constant pH replica-exchange molecular dynamics and quantum mechanics/molecular mechanics umbrella sampling quantitatively characterize the ligands protonation-state change upon binding to the eDHFR active site. Thermodynamic integration simulations using alternative alchemical pathways, thermodynamic cycles, and protonation-state assignments were evaluated for predicting light-responsive affinity differentials and substituent effects. Direct cis-to-trans transformations with explicit treatment of environment-dependent protonation states best reproduce experimental trends. Compound-to-compound pathways are less reliable because force-field inaccuracies introduce large pK errors that are difficult to correct when protonation/deprotonation processes implicitly enter the thermodynamic cycle. TI simulations that ignore binding-induced protonation-state changes fail to consistently reproduce experimental trends. Protein-ligand and ligand-water interaction analyses further reveal the energetic and structural origins of isomer-dependent binding. This study establishes a systematic free-energy method for designing ionizable photoswitches in photopharmacology.

pharmacology and toxicology↗

bioRxiv2025

Mechanistic Understanding of Protein-MOF Integration through Surfactant-Driven Interfacial Design

Integration of proteins into metal-organic frameworks (Protein@MOF) represents an effective method for protein stabilization, with rising demand across material and biomedical sciences. However, the molecular mechanism of protein-MOF interactions remains unsettled due to challenges in developing a general platform to systematically investigate such interactions, hindering improvements in their chemical and physical properties. Here, we develop a surfactant-guided strategy to modulate the assembly of protein@MOF through interfacial design. We discovered that the interfacial environment between proteins and MOFs is the primary factor determining encapsulation efficiency, structural retention, and functional performance. Lipid-based non-ionic surfactants such as glycerol monooleate (GMO) increase the proteins solvent-accessible surface area (SASA), suggesting partial remodeling of the protein surface and hydration shell. GMO at the interface of protein@MOF results in a 20% improvement in protein encapsulation and a 30% increase in MOF growth rate. All-atom molecular dynamics simulations reveal domain-specific interactions between GMO and flexible surface residues on protein in a concentration-dependent manner, involving both electrostatic and hydrophobic contacts. This work offers new molecular insights into how surfactant-driven interfacial design fine-tunes the stability of protein@MOF, laying the foundation for robust alternatives to lipid nanodiscs for membrane protein stabilization, and protein-based platforms for drug-delivery, biocatalysis, and biosensing.

biophysics↗