Structure, energetics and dynamics in crowded amino acid solutions: a molecular dynamics study

In Silico View of Crowding: Biomolecular Processes to Nanomaterial Design

It is widely accepted that deciphering biomolecular structure and function requires going beyond the single-molecule or single-complex paradigm. The densely packed macromolecules, cosolutes, and metabolites in the living cell impose crowding effects on the biomolecular structure and dynamics that need to be accounted for. Molecular simulations have proven to be a powerful tool to advance the current molecular-level understanding of such a highly concentrated, complex milieu. This Mini-Review focuses on summarizing the understanding achieved so far for the effects of crowding on biomolecular processes using computational methods, along with highlighting a new direction in employing crowding as a tool for tunable nanomaterial design. The two schools of thought that form the pillars of the current understanding of crowding effects are discussed. The investigation of crowded solutions using physics-based models that encompass different time and length scales to mimic the intracellular environment are described. The limitations and challenges faced by the current models and simulation methods are addressed, highlighting the gaps to be filled for better agreement with experiments. Crowding can also act as an effective tool to modulate the structure-property-function relationships of nanomaterials, leading to the development of novel functional materials. A few recent studies, mostly experimental, have been summarized in this direction. The Mini-Review concludes with an outlook for future developments in this field in order to enable accurate mimicking of the intracellular environment using simulations and to bridge the gap between biological processes and nanomaterial design.

Differential local ordering of mixed crowders determines effective size and stability of ss-DNA capped gold nanoparticle

Understanding the influence of a crowded intracellular environment on the structure and solvation of DNA functionalized gold nanoparticles (ss-DNA AuNP) is necessary for designing applications in nanomedicine. In this study, the effect of single (Gly, Ser, Lys) and mixture of amino acids (Gly+Ser, Gly+Lys, Ser+Lys) at crowded concentrations is examined on the structure of the ss-DNA AuNP using molecular dynamics simulations. Using the structural estimators such as pair correlation functions and ligand shell positional fluctuations, the solvation entropy is estimated. Combining the AuNP-solvent interaction energy with the solvation entropy estimates, the free energy of solvation of the AuNP in crowded solutions is computed. The solvation entropy favours the solvation free energy which becomes more favourable for larger effective size of AuNP in crowded solutions relative to that in water. The effective size of AuNP depends on the different propensity of the crowders to adsorb on Au surface, with the smallest crowder (Gly) having the highest propensity inducing the least effective AuNP size as compared to other single crowder solutions. In mixed crowded solutions of amino acids of variable size and chemistry, distinctive local adsorption of the crowders on the gold surface is observed that controls the additive or non-additive crowding effects which govern an increase (in Gly+Ser) or decrease (in Gly+Lys) in nanoparticle effective size respectively. The results shed light into the fundamental understanding of the influence of intracellular crowding on structure of ss-DNA AuNP and plausible employability of crowding as a tool to design programmable self-assembly of functionalized nanoparticles.