Importance of Hydrogen Bonding in Crowded Environments: A Physical Chemistry Perspective

Abstract

Cells are heterogeneous on every length and time scale; cytosol contains thousands of proteins, lipids, nucleic acids, and small molecules, and molecular interactions within this crowded environment determine the structure, dynamics, and stability of biomolecules. For decades, the effects of crowding at the atomistic scale have been overlooked in favor of more tractable models largely based on thermodynamics. Crowding can affect the conformations and stability of biomolecules by modulating water structure and dynamics within the cell, and these effects are nonlocal and environment dependent. Thus, characterizing water’s hydrogen-bond (H-bond) networks is a critical step toward a complete microscopic crowding model. This perspective provides an overview of molecular crowding and describes recent time-resolved spectroscopy approaches investigating H-bond networks and dynamics in crowded or otherwise complex aqueous environments. Ultrafast spectroscopy combined with atomistic simulations has emerged as a powerful combination for studying H-bond structure and dynamics in heterogeneous multicomponent systems. We discuss the ongoing challenges toward developing a complete atomistic description of macromolecular crowding from an experimental as well as a theoretical perspective.

Unveiling the Rational Development of Stimuli-Responsive Silk Fibroin-Based Ionogel Formulations

“…We suggest that IL inclusion promotes the formation of diverse ionogels via electrostatic, inter- and intramolecular hydrogen bonding interactions. ,, We consider that for the [Cho]­[Cl]-ionogel formulations, of highest ionic strength, [Cho]­[Cl] incorporation could result in surface charge accumulation on the silk fibroin chains and weak intermolecular hydrogen bonding interactions. ,− This would explain our findings of higher T ionogel values, lower phenobarbital solubility, and impeded [Cho]­[Cl]-ionogel formation. In contrast, the extended structure of the dihydrogen phosphate anions could contribute to the formation of strong intermolecular hydrogen bonding networks and steric effects. − This aligns with our observations of a shorter formation period, greater strength, structural and energetic stability for the [Cho]­[DHP]-ionogels compared to the [Cho]­[Cl]-ionogels. The acetate anions possess more compact structures relative to the dihydrogen phosphate anions, and the ionic strength of the [Cho]­[OAc]-ionogel formulations is lower compared to the [Cho]­[Cl]-ionogel formulations.…”

“…Following this logic, [Cho]­[DHP] could most effectively anchor to the silk fibroin chains and facilitate the diffusion of the PVP molecules, resulting in enhanced macromolecular confinement effects. Furthermore, potential steric effects of the extended structure of the dihydrogen phosphate anions would be compensated for, and the structural and energetic stabilization of the PVP-[Cho]­[DHP]-ionogels would be increased. − This aligns with our finding of strong intermolecular hydrogen bonding interactions, greatest strength, and least delayed period for the formation of the PVP-[Cho]­[DHP]-ionogel formulations containing glycerol. The inclusion of glycerol molecules, containing multiple hydroxyl groups, likely enhanced the intermolecular hydrogen bonding interactions between the silk fibroin chains, disaccharides, surfactants, and amino acid molecules, in the absence and presence of PVP. ,− Thus, glycerol containing formulations could exhibit strong intra- and intermolecular hydrogen bonds, and enhanced macromolecular crowding and confinement effects, yielding the formation of ionogels of greater strength, and higher structural and energetic stability.…”

Effects of External Perturbations on Protein Systems: A Microscopic View

“…Their nonspecific interactions and cluster formation contribute to the high viscosity in the crowded solution . The molecular level understanding through computational studies further shows that the presence of a crowder or a cosolvent (effector of solvent viscosity) significantly changes the structure and dynamics of the hydration shell and can reduce the diffusivity and the dielectric constant of solvent waters. − It is reported that, due to crowding effects, peptide interfacial waters can behave as a glue (or adhesive) for assembly with the increase in the lifetimes of water–water hydrogen bonds. − …”

“… 158 − 162 It is reported that, due to crowding effects, peptide interfacial waters can behave as a glue (or adhesive) for assembly with the increase in the lifetimes of water–water hydrogen bonds. 163 − 168 …”

Ultrafast Spectroscopy Reveals Slow Water Dynamics in Biocondensates

“…Water constitutes about 70% of the condensate volume, and water molecules within the condensate either directly solvate the biomolecules or are confined to nanometer-scale pores and constrained by strong electrostatic interactions. , These crowded environments, with high biomolecule concentrations within the BMCs disrupt the long-range H-bond networks present in pure water and instead produce dynamics significantly different from the bulk, analogous to the crowded environments in the cytosol. , Considering the importance of H-bonding in biological processes, it is essential to directly probe the local environments and dynamics within the condensate phase, understand the molecular-level structure, and elucidate the interactions that lead to phase separation. From a biophysical perspective, it is important to understand the balance of thermodynamic driving forces that stabilize the condensate and the behavior of biomolecules within the condensate matrix. − …”