Osmolyte-Induced Collapse of a Charged Macromolecule

Abstract

In the recent surge of investigations on osmolyte-induced conformational landscape of hydrophobic macromolecules notwithstanding, there is a lack of understanding of how the presence of Coulombic charges in the macromolecule dictates its own conformational preference in aqueous media of osmolyte. Toward this end, in this work, we have computationally simulated the trimethyl amine N-oxide (TMAO)-induced collapse behavior of a charge-neutral polymer by varying the number of oppositely charged monomeric beads of a given charge density. From our free-energy-based analysis, at low charge density, there emerges a nonmonotonic trend in the extent of osmolyte-induced protection of collapsed conformation of the charge-neutral polymer as a function of the number of periodically distributed charged monomers: specifically, we observe that, at low charge density, with incremental introduction of oppositely charged monomers in the charge-neutral polymer, the process of osmolyte-induced polymer collapse first gets free-energetically destabilized relative to that in uncharged polymer. However, with further increase in the number of charged monomers of low charge density, there is a recurrence of osmolyte-induced stabilization of polymer collapse. On the contrary, the nonmonotonic trend in osmolyte-induced polymer collapse across the number of charged monomer beads diminishes with an increase in charge density: the aqueous TMAO solution becomes a denaturant of the polymer collapse at higher charge distribution in charge-neutral polymer with higher charge density. A molecular-level analysis of the polymer−osmolyte interaction reveals that the differential interaction of nitrogen and oxygen atoms of TMAO with the charged polymer beads, together with the competing effect of polymer−TMAO dispersion interaction and electrostatic interaction, holds the key in dictating the trend in the osmolyte-induced protection of the polymer collapse across various charge densities and charge distributions.

Unifying the Ambivalent Mechanisms of Protein-Stabilising Osmolytes

“…Moreover, the current work's demonstration that protein-stabilizing osmolyte may have ambivalent interactions with the proteins, can have possible implication in their mechanistic action in modulating protein-protein interactions. 29,[43][44][45] Recent experiments in these directions have shown that osmolyte and non-osmolytes may have a distinct role in perturbing charge-mediated inter-protein interactions 43 and that zwitterionic osmolytes can resurrect the electrostatic interactions among charged surfaces, with low temperature playing an important role. 44,46,47 Future investigation in the possible molecular mechanism of osmolyte-induced protein-protein interaction and its possible modulation of liquid-liquid protein phase separation 48 can provide interesting insights.…”

“…Since then, the idea of stabilization of hydrophobic interaction via preferential binding of TMAO with the surface, in contrast to its exclusion from the surface, has received regular attention in multiple subsequent studies. 18,[22][23][24][25][26][27][28][29] However, these works have been mostly limited to model polymer and not been validated in case of realistic proteins, until recently.…”

Nonaffine Displacements Encode Collective Conformational Fluctuations in Proteins

“…The polymer mimics bead-in-a-spring model with a total of 32 beads connected by harmonic bonds and angles, the details of which are documented else-where. 29 The polymer consists of alternative positive and negative charges on the beads in a periodic fashion . Apart from the electrostatic interaction, the polymer beads additionally interact with each other and the aqueous media via lenard Jones (LJ) interaction.…”

“…found in our previous work. 29 We have run 200 independent simulations, each 30 ns long, by starting with diverse conformation of the polymer.…”

Non-affine displacements encode collective conformational fluctuations in proteins

“…Computational models of the three systems studied in the current work: a) 32bead model polymer, b) C-terminal domain of GB1 β-hairpin (residues 41-56) and c)Bovine pancreatic trypsin inhibitor (BPTI) protein found in our previous work 29. We have run 200 independent simulations, each 30 ns long, by starting with diverse conformation of the polymer.The 16-residue long peptide Ace-41 GEWTYDDATKTFTVTE 56 -Nme, as taken out from the full-length GB1 protein NMR structure (PDB: 1GB1 31 ) was modelled using AMBER03-STAR 32,33 forcefield and solvated in a truncated octahedron simulation cell containing 984 TIP3P 34 water molecules and electroneutralized.…”