Cosolvent Effects on Polymer Hydration Drive Hydrophobic Collapse

Contrasting behavior of urea in strengthening and weakening confinement effects on polymer collapse

Biomolecules inhabit a crowded living cell that is packed with high concentrations of cosolutes and macromolecules that result in restricted, confined volumes for biomolecular dynamics. To understand the impact of crowding on the biomolecular structure, the combined effects of the cosolutes (such as urea) and confinement need to be accounted for. This study involves examining these effects on the collapse equilibria of three model 32-mer polymers, which are simplified models of hydrophobic, charge-neutral, and uncharged hydrophilic polymers, using molecular dynamics simulations. The introduction of confinement promotes the collapse of all three polymers. Interestingly, addition of urea weakens the collapse of the confined hydrophobic polymer, leading to non-additive effects, whereas for the hydrophilic polymers, urea enhances the confinement effects by enhancing polymer collapse (or decreasing the polymer unfolding), thereby exhibiting an additive effect. The unfavorable dehydration energy opposes collapse in the confined hydrophobic and charge-neutral polymers under the influence of urea. However, the collapse is driven mainly by the favorable change in polymer-solvent entropy. The confined hydrophilic polymer, which tends to unfold in bulk water, is seen to have reduced unfolding in the presence of urea due to the stabilizing of the collapsed state by urea via cohesive bridging interactions. Therefore, there is a complex balance of competing factors, such as polymer chemistry and polymer-water and polymer-cosolute interactions, beyond volume exclusion effects, which determine the collapse equilibria under confinement. The results have implications to understand the altering of the free energy landscape of proteins in the confined living cell environment.

Osmolyte-induced conformational stabilization of a hydrophobic polymer

Elucidating the mechanistic role of osmolytes on conformations of hydrophobic prototypical macromolecules in principle is the stepping stone towards understanding the effect of osmolytes on proteins. Motivated by this, we use equilibrium simulations and umbrella sampling techniques to dissect the underlying mechanism of osmolyte-induced conformational stability of a hydrophobic polymer. Our results unveil a remarkable osmolyte-dependent conformational stabilization of the polymer. In an aqueous solution of 4 M choline chloride (ChCl), the polymer has an even more compact structure than in water. On the other hand, an aqueous solution of 8 M urea stabilizes the extended state of the polymer. Interestingly, the polymer adopts an intermediate hairpin conformation in a mixed osmolyte solution of 4 M ChCl and 8 M urea in water due to the interplay of ChCl and urea. Our simulations identify the relative accumulation of water and the hydrophilic part of choline or preferential binding of urea near the collapsed and the extended states, respectively. Analyses split out the enthalpic and entropic contributions to the overall free energy. This decides the stabilization of the preferred conformation in the chosen osmolyte solution. Our simulations show that in an aqueous solution of ChCl, the hairpin state is stabilized by entropy gain. In contrast, the enthalpic contribution stabilizes the hairpin state in mixed environments. However, a collapsed state is energetically not favored in the presence of urea. In brief, via employing an in silico approach, the current findings indicate the importance of osmolytes in stabilizing the conformational states of hydrophobic polymers.

Optimized Collective Variable for Collapse Transition in Linear Hydrophobic Polymers: Importance of Hydration Water and End-to-End Distance

Choosing an appropriate collective variable (CV) for any biomolecular process is a challenging task. Researchers are developing methods to solve this issue using a variety of methodologies, most recently using machine learning (ML) methods. In this work, we investigate the mechanism of collapse transition across various lengths of polymer systems through adaptively sampled multiple short trajectories utilizing the Time Lagged Independent Component Analysis (TICA) framework. From TICA analysis, it is revealed that the radius of gyration (Rg) and end-to-end distance serve as good order parameters (OPs) for these systems describing overall energy landscapes. Markov state model (MSM) and mean first passage time (MFPT) analysis suggest that hydration water (Nw) plays a determining role in dictating the time scale and barrier for the collapsed transition for the C40 system. P-fold analysis on identifying transition state ensembles (TSE) identified by committor analysis also strengthens the role of Nw in such a transition. TICA, MSM, and committor analyses on the collapse transition for C45 reveal similarities with C40 systems in different aspects. Furthermore, we propose a pipeline integrating XGBoost regression along with an interpretable ML model, Shapley Additive exPlanation (SHAP) to precisely elucidate the contribution of each OP locally at the TSE. Through this approach, we observe that the collapse transition is primarily driven by Nw for both polymer systems. A carefully designed protocol for the collapsed transition of C60 systems indirectly reiterates the above result. Overall, our results suggest that while the end-to-end distance should be considered for better resolution of metastable states in the landscape, Nw is the crucial coordinate to be used in enhanced sampling for the exploration of actual collapse transitions for linear hydrophobic polymer systems. The Python code for analyzing the contribution of different OPs in the TSE using an ML-aided protocol is available on GitHub (https://github.com/saikat-ai/linear_polymer_project).

Effects of Polymer Architecture and Charged Molecular Crowders on Hydrophobic Polymer Collapse

Accounting for the crowding effects inside a living cell is crucial to obtain a comprehensive view of the biomolecular processes and designing responsive polymer-based materials for biomedical applications. These effects have long been synonymous with the entropic volume exclusion effects. The role of soft, attractive intermolecular interactions remains elusive. Here, we investigate the effects of model cationic and anionic hydrophobic molecular crowders on the collapse equilibrium of uncharged model polymers using molecular dynamics simulations. Particularly, the effect of polymer architecture is explored where a 50-bead linear polymer model (Poly-I) and a branched polymer model (Poly-II) with nonpolar side chains are examined. The collapse of Poly-I is found to be highly favorable than in Poly-II in neat water. Addition of anionic crowders strengthens hydrophobic collapse in Poly-I, whereas collapse of Poly-II is only slightly favored over that in neat water. The thermodynamic driving forces are quite distinct in water. Collapse of Poly-I is driven by the favorable polymer-solvent entropy change (due to loss of waters to bulk on collapse), whereas collapse of Poly-II is driven by the favorable polymer-solvent energy change (due to favorable intrapolymer energy). The anionic crowders support the entropic mechanism for Poly-I by acting like surfactants, redirecting water dipoles toward themselves, and preferentially adsorbing on the Poly-I surface. In the case of Poly-II, the anionic crowders are loosely bound to polymer side chains, and loss of crowders and waters to the bulk on polymer collapse reduces the entropic penalty, thereby making collapse free energy slightly more favorable than in neat water. The results indicate the discriminating behavior of anionic crowders to strengthen the hydrophobic collapse. It is related to the structuring of water molecules around the termini and the central region of the two polymers. The results address the modulation of hydrophobic hydration by weakly hydrated ionic hydrophobes at crowded concentrations.

Co-Solutes Induced Changes in the Properties of Polymeric Solution and Water Dynamics

In this paper we are addressing the co-solute-induced changes in the properties of an aqueous solution of a block copolymer. Due to the preferential interaction of different co-solute with different regions of the block copolymer, the changes were observed in both the physical properties and water dynamics. The modulation of both the physical properties and water dynamics was monitored using different spectroscopic techniques. Different co-solutes affect micellar properties of copolymer to a different extent signifying their interactions with different regions within the copolymer. The solvent relaxation dynamics were also modulated with the additions of different co-solutes. The change in free-energy (ΔGbf) and rate constant for bound to free water interconversion (kbf) in a copolymeric micelle was calculated which gets affected by the addition of co-solutes. The calculated kbf suggests that betaine, sarcosine, TMAO, and GnHCl favor the ordering of water molecules around the micelle and are excluded from the micellar surface whereas, urea favors the formation of free-water molecules rather than the structurally ordered bound water molecules around the micelle by accumulating at the micellar surface. Among the added methylamines trimethylamine N-oxide affected the water dynamics and its kinetics most profoundly. The protective property of GnHCl was revealed.

Interactions of adsorbing cosolutes with hydrophobic hydration shells

The analysis of water density fluctuations in the hydration shell of nonpolar solutes provides insights into water-mediated interactions, especially hydrophobic interactions. These fluctuations are sensitive to small perturbations due to changes in thermodynamic conditions, such as temperature and pressure, but also to the presence of cosolutes, such as salts or small organic molecules. Herein, we investigate the effect of two classes of adsorbing cosolutes, using urea and methanol as representatives, on the fluctuations in energy and solvent density within the solvation shell of a model extended hydrophobic solute. We focus on the interactions of the cosolutes with the hydrophobic hydration shell, rather than with the solute itself, which though important remain largely unexplored. We calculate and analyze the interfacial partial molar energy of the cosolute, using a methodology based on the small system method. This approach provides correlated solvent density and energy fluctuations and allows us to decompose them into contributions due to interactions between the different components present in the solvation shell of the solute. The results show that adsorbed urea molecules interact more favorably with water than nonadsorbed urea molecules, which leads to the attenuation of interfacial density fluctuations and thus to the stabilization of the solvation shell. By contrast, the adsorbed methanol molecules interact preferably with other methanol molecules in the solvation shell, leading to a nano-phase segregated structure, which enhances interfacial fluctuations.

Molecular Crowders Can Induce Collapse in Hydrophilic Polymers via Soft Attractive Interactions

A comprehensive understanding of protein folding and biomolecular self-assembly in the intracellular environment requires obtaining a microscopic view of the crowding effects. The classical view of crowding explains biomolecular collapse in such an environment in terms of the entropic solvent excluded volume effects subjected to hard-core repulsions exerted by the inert crowders, neglecting their soft chemical interactions. In this study, the effects of nonspecific, soft interactions of molecular crowders in regulating the conformational equilibrium of hydrophilic (charged) polymers are examined. Using advanced molecular dynamics simulations, collapse free energies of an uncharged, a negatively charged, and a charge-neutral 32-mer generic polymer are computed. The strength of the polymer-crowder dispersion energy is modulated to examine its effect on polymer collapse. The results show that the crowders preferentially adsorb and drive the collapse of all three polymers. The uncharged polymer collapse is opposed by the change in solute-solvent interaction energy but is overcompensated by the favorable change in the solute-solvent entropy as observed in hydrophobic collapse. However, the negatively charged polymer collapses with a favorable change in solute-solvent interaction energy due to reduction in the dehydration energy penalty as the crowders partition to the polymer interface and shield the charged beads. The collapse of a charge-neutral polymer is opposed by the solute-solvent interaction energy but is overcompensated by the solute-solvent entropy change. However, for the strongly interacting crowders, the overall energetic penalty decreases since the crowders interact with polymer beads via cohesive bridging attractions to induce polymer collapse. These bridging attractions are found to be sensitive to the binding sites of the polymer, since they are absent in the negatively charged or uncharged polymers. These interesting differences in thermodynamic driving forces highlight the crucial role of the chemical nature of the macromolecule as well as of the crowder in determining the conformational equilibria in a crowded milieu. The results emphasize that the chemical interactions of the crowders should be explicitly considered to account for the crowding effects. The findings have implications in understanding the crowding effects on the protein free energy landscapes.

Influence of TMAO and Pressure on the Folding Equilibrium of TrpCage

Trimethylamine-N-oxide (TMAO) is an osmolyte known for its ability to counteract the pressure denaturation of proteins. Computational studies addressing the molecular mechanisms of TMAO's osmolyte action have however focused exclusively on its protein-stabilizing properties at ambient pressure, neglecting the changes that may occur under high-pressure conditions where TMAO's hydration structure changes to that of increased water binding. Here, we present the first study on the combined effect of pressure and TMAO on a mini-protein, TrpCage. The results showed that at high pressures, nonpolar residues packed less tightly and the salt bridge of TrpCage was destabilized. This effect was mitigated by TMAO which was found to be strongly depleted from the protein/water interface at 1 kbar than at 1 bar ambient pressure, thus counterbalancing the thermodynamically unfavorable effect of elevated pressure in the free energy of folding. TMAO was depleted from charged groups, like the salt bridge-forming ones, and accumulated around hydrophobic groups. Still, it stabilized both kinds of interactions. Furthermore, enthalpically favorable TrpCage-water hydrogen bonds were reduced in the presence of TMAO, causing a stronger destabilization of the unfolded state than the folded state. This shifted the protein-folding equilibrium toward the folded state. Therefore, TMAO showed stabilizing effects on different kinds of groups, which were partially enhanced at high pressures.

The protein-stabilizing effects of TMAO in aqueous and non-aqueous conditions

We present a new water-dependent molecular mechanism for the widely-used protein stabilizing osmolyte, trimethylamine N-oxide (TMAO), whose mode of action has remained controversial. Classical interpretations, such as osmolyte exclusion from the vicinity of protein, cannot adequately explain the behavior of this osmolyte and were challenged by recent data showing the direct interactions of TMAO with proteins, mainly via hydrophobic binding. Solvent effect theories also fail to propose a straightforward mechanism. To explore the role of water and the hydrophobic association, we disabled osmolyte-protein hydrophobic interactions by replacing water with hexane and using lipase enzyme as an anhydrous-stable protein. Biocatalysis experiments showed that under this non-aqueous condition, TMAO does not act as a stabilizer, but strongly deactivates the enzyme. Molecular dynamics (MD) simulations reveal that TMAO accumulates near the enzyme and makes many hydrogen bonds with it, like denaturing osmolytes. Some TMAO molecules even reach the active site and interact strongly with the catalystic traid. In aqueous solvent, the enzyme functions well: the extent of TMAO interactions is reduced and can be divided into both polar and non-polar terms. Structural analysis shows that in water, some TMAO molecules bind to the enzyme surface like a surfactant. We show that these interactions limit water-protein hydrogen bonds and unfavorable water-hydrophobic surface contacts. Moreover, a more hydrophobic environment is formed in the solvation layer, which reduces water dynamics and subsequently, rigidifies the backbone in aqueous solution. We show that osmolyte amphiphilicity and protein surface heterogeneity can address the weaknesses of exclusion and solvent effect theories about the TMAO mechanism.

Temperature induced change of TMAO effects on hydrophobic hydration

The effect of trimethylamine-N-oxide (TMAO) on hydrophobic solvation and hydrophobic interactions of methane has been studied with Molecular Dynamics simulations in the temperature range between 280 and 370 K at 1 bar ambient pressure. We observe a temperature transition in the effect of TMAO on the aqueous solubility of methane. At low temperature (280 K), methane is preferentially hydrated, causing TMAO to reduce its solubility in water, while above 320 K, methane preferentially interacts with TMAO, causing TMAO to promote its solubility in water. Based on a statistical-mechanical analysis of the excess chemical potential of methane, we find that the reversible work of creating a repulsive methane cavity opposes the solubility of methane in TMAO/water solution more than in pure water. Below 320 K, this solvent-excluded volume effect overcompensates the contribution of methane–TMAO van der Waals interactions, which promote the solvation of methane and are observed at all temperatures. These van der Waals interactions with the methyl groups of TMAO tip the balance above 320 K where the effect of TMAO on solvent-excluded volume is smaller. We furthermore find that the effective attraction between dissolved methane solutes increases with the increasing TMAO concentration. This observation correlates with a reduction in the methane solubility below 320 K but with an increase in methane solubility at higher temperatures.

Solvation shell thermodynamics of extended hydrophobic solutes in mixed solvents

The ability of various cosolutes and cosolvents to enhance or quench solvent density fluctuations at solute–water interfaces has crucial implications on the conformational equilibrium of macromolecules such as polymers and proteins. Herein, we use an extended hydrophobic solute as a model system to study the effect of urea and methanol on the density fluctuations in the solute’s solvation shell and the resulting thermodynamics. On strengthening the solute–water/cosolute repulsive interaction, we observe distinct trends in the mutual affinities between various species in, and the thermodynamic properties of, the solvation shell. These trends strongly follow the respective trends in the preferential adsorption of urea and methanol: solute–water/cosolute repulsion strengthens, urea accumulation decreases, and methanol accumulation increases. Preferential accumulation of urea is found to quench the density fluctuations around the extended solute, leading to a decrease in the compressibility of the solvation shell. In contrast, methanol accumulation enhances the density fluctuations, leading to an increase in the compressibility. The mode of action of urea and methanol seems to be strongly coupled to their hydration behavior. The observations from this simple model is discussed in relation to urea driven swelling and methanol induced collapse of some well-known thermo-responsive polymers.

Hydrophobic association and solvation of neopentane in urea, TMAO and urea-TMAO solutions

A detailed knowledge of hydrophobic association and solvation is crucial for understanding the con-formational stability of proteins and polymers in osmolyte solutions. Using molecular dynamics simulations, it is found that the hydrophobic association of neopentane molecules is greater in a mixed urea-TMAO-water solution in comparison to that in 8 M urea solution, 4 M TMAO solution and neat water. The neopentane association in urea solution is greater than that in TMAO solution or neat water. We find the association is even less in TMAO solution than pure water. From free energy calculations, it is revealed that the neopentane sized cavity creation in mixed urea-TMAO-water is most unfavorable and that causes the highest hydrophobic association. The cavity formation in urea solution is either more unfavorable or comparable to that in TMAO solution. Importantly, it is found that the population of neopentane-neopentane contact pair and the free energy contribution for the cavity formation step in TMAO solution are very sensitive towards the choice of TMAO force-fields. A careful construction of TMAO force-fields is important for studying the hydrophobic association. Interestingly it is observed that the total solute-solvent dispersion interaction energy contribution is always the most favorable in mixed urea-TMAO-water. The magnitude of this interaction energy is greater in urea solution relative to TMAO solution for two different force-fields of TMAO, whereas the lowest value is obtained in pure water. It is revealed that the extent of the overall hydrophobic association in osmolyte solutions is mainly governed by the cavity creation step and it nullifies the contribution coming from the solute-solvent interaction contribution.

Small-to-large length scale transition of TMAO interaction with hydrophobic solutes

We report the effect of trimethylamine N-oxide (TMAO) on the solvation of nonpolar solutes in water studied with molecular dynamics (MD) simulations and free-energy calculations. The simulation data indicate the occurrence of a length scale crossover in the TMAO interaction with repulsive Weeks-Chandler-Andersen (WCA) solutes: while TMAO is depleted from the hydration shell of a small WCA solute (methane) and increases the free-energy cost of solute-cavity formation, it preferentially binds to a large WCA solute (α-helical polyalanine), reducing the free-energy cost of solute-cavity formation via a surfactant-like mechanism. Significantly, we show that this surfactant-like behaviour of TMAO reinforces the solvent-mediated attraction between large WCA solutes by means of an entropic force linked to the interfacial accumulation of TMAO. Specifically, this entropic force arises from the natural tendency of adsorbed TMAO molecules to mix back into the bulk. It therefore favours solute-solute contact states that minimise the surface area exposed to the solvent and have a small overall number of TMAO molecules adsorbed. In contrast to the well-known depletion force, its effect is compensated by enthalpic solute-solvent interactions. Correspondingly, the hydrophobic association free energy of the large α-helical solutes passes through a minimum at low TMAO concentration when cohesive solute-solvent van der Waals interactions are considered. The observations reported herein are reminiscent to cosolvent effects on hydrophobic polymer coil-globule collapse free energies (Bharadwaj et al., Commun. Chem. 2020, 3, 165) and may be of general significance in systems whose properties are determined by hydrophobic self-assembly.

Direct Calculation of Entropic Components in Cohesive Interaction Free Energies

Cohesive interaction free energies entail an entropic component related to fluctuations of the energy associated with the attractive portion of the solute-solvent potential. The corresponding "fluctuation entropy" is fundamental in the solvation thermodynamics of macromolecular solutes and is linked to interfacial solvent density fluctuations and hydrophobic effects. Since the direct calculation of fluctuation entropy in molecular simulations is hampered by the poor sampling of high-energy tails in the solute-solvent energy distribution, indirect, and often approximate, routes for the calculation of fluctuation entropy are usually required, involving the modeling of geometrically frozen repulsive solute cavities in thermodynamic integration approaches. Herein, we propose a method to directly compute the fluctuation entropy by employing indirect umbrella sampling (INDUS). To validate the method, we consider model systems consisting of subnanometer oil droplets in water for which the fluctuation entropy can be computed exactly using indirect methods. The fluctuation entropy calculated with the newly proposed direct method agrees with the indirect reference calculations. We also observe that the solvation free energy and the contribution of the fluctuation entropy to it are of comparable magnitudes, particularly for larger oil droplets (∼1 nm). The proposed method can readily be employed for flexible macromolecular solutes and systems with extended hydrophobic surfaces or in the vicinity of a dewetting transition.

Length-Scale Effects in Hydrophobic Polymer Collapse Transitions

The study of molecular mechanisms for cosolvent-driven hydrophobic polymer collapse transitions in water is of pivotal importance in the field of smart responsive materials. Computational studies together with complementary experimental data have led to the discovery and understanding of new phenomena in recent years. However, elementary mechanisms, generally contributing to polymer coil-globule transitions in different classes of cosolvent-water systems, remain elusive due to compensating energy-entropy effects. Herein, I discuss the role of length scales in polymer solubility problems. New ideas on surfactant mechanisms are discussed based on examples in which these mechanisms drive polymer swelling or collapse.

Characterizing the Interplay between Polymer Solvation and Conformation

Conformational transitions of flexible molecules, especially those driven by hydrophobic effects, tend to be hindered by desolvation barriers. For such transitions, it is thus important to characterize and understand the interplay between solvation and conformation. Using specialized molecular simulations, here we perform such a characterization for a hydrophobic polymer solvated in water. We find that an external potential, which unfavorably perturbs the polymer hydration waters, can trigger a coil-to-globule or collapse transition, and that the relative stabilities of the collapsed and extended states can be quantified by the strength of the requisite potential. Our results also provide mechanistic insights into the collapse transition, highlighting that the bottleneck to polymer collapse is the formation of a sufficiently large cluster, and the collective dewetting of such a cluster. We also study the collapse of the hydrophobic polymer in octane, a nonpolar solvent, and interestingly, we find that the mechanistic details of the transition are qualitatively similar to that in water.

An interplay of excluded-volume and polymer-(co)solvent attractive interactions regulates polymer collapse in mixed solvents

Cosolvent effects on the coil-globule transitions in aqueous polymer solutions are not well understood, especially in the case of amphiphilic cosolvents that preferentially adsorb on the polymer and lead to both polymer swelling and collapse. Although a predominant focus in the literature has been placed on the role of polymer-cosolvent attractive interactions, our recent work has shown that excluded-volume interactions (repulsive interactions) can drive both preferential adsorption of the cosolvent and polymer collapse via a surfactant-like mechanism. Here, we further study the role of polymer-(co)solvent attractive interactions in two kinds of polymer solutions, namely, good solvent (water)-good cosolvent (alcohol) (GSGC) and poor solvent-good cosolvent (PSGC) solutions, both of which exhibit preferential adsorption of the cosolvent and a non-monotonic change in the polymer radius of gyration with the addition of the cosolvent. Interestingly, at low concentrations, the polymer-(co)solvent energetic interactions oppose polymer collapse in the GSGC solutions and contrarily support polymer collapse in the PSGC solutions, indicating the importance of the underlying polymer chemistry. Even though the alcohol molecules are preferentially adsorbed on the polymer, the trends of the energetic interactions at low cosolvent concentrations are dominated by the polymer-water energetic interactions in both the cases. Therefore, polymer-(co)solvent energetic interactions can either reinforce or compensate the surfactant-like mechanism, and it is this interplay that drives coil-to-globule transitions in polymer solutions. These results have implications for rationalizing the cononsolvency transitions in real systems such as polyacrylamides in aqueous alcohol solutions where the understanding of microscopic driving forces is still debatable.

Bottom-Up View of the Mechanism of Action of Protein-Stabilizing Osmolytes

The molecular mechanism of osmolytes on the stabilization of native states of protein is still controversial irrespective of extensive studies over several decades. Recent investigations in terms of experiments and molecular dynamics simulations challenge the popular osmophobic model explaining the mechanistic action of protein-stabilizing osmolytes. The current Perspective presents an updated view on the mechanistic action of osmolytes in light of resurgence of interesting experiments and computer simulations over the past few years in this direction. In this regard, the Perspective adopts a bottom-up approach starting from hydrophobic interactions and eventually adds complexity in the system, going toward the protein, in a complex topology of hydrophobic and electrostatic interactions. Finally, the Perspective unifies osmolyte-induced protein conformational equilibria in terms of preferential interaction theory, irrespective of individual preferential binding or exclusion of osmolytes depending on different osmolytes and protein surfaces. The Perspective also identifies future research directions that can potentially shape this interesting area.

A cosolvent surfactant mechanism affects polymer collapse in miscible good solvents

The coil-globule transition of aqueous polymers is of profound significance in understanding the structure and function of responsive soft matter. In particular, the remarkable effect of amphiphilic cosolvents (e.g., alcohols) that leads to both swelling and collapse of stimuli-responsive polymers has been hotly debated in the literature, often with contradictory mechanisms proposed. Using molecular dynamics simulations, we herein demonstrate that alcohols reduce the free energy cost of creating a repulsive polymer-solvent interface via a surfactant-like mechanism which surprisingly drives polymer collapse at low alcohol concentrations. This hitherto neglected role of interfacial solvation thermodynamics is common to all coil-globule transitions, and rationalizes the experimentally observed effects of higher alcohols and polymer molecular weight on the coil-to-globule transition of thermoresponsive polymers. Polymer-(co)solvent attractive interactions reinforce or compensate this mechanism and it is this interplay which drives polymer swelling or collapse.

Small crowder interactions can drive hydrophobic polymer collapse as well as unfolding

Biomolecules evolve and function in the intracellular crowded environment that is densely packed with macromolecules. Yet, a microscopic understanding of the effects of such an environment on the conformational preferences of biomolecules remains elusive. While prior investigations have attributed crowding effects mainly to the excluded volume (size) effects of the crowders, very little is known about the effects exerted due to their chemical interactions. In this study, crowding effects of tri-alanine peptides on the collapse equilibria of generic hydrophobic polymer are investigated using molecular dynamics simulations. The role of weak, non-specific, attractive polymer-crowder interactions in modulating the polymer collapse equilibria is examined. The results highlight that crowding effects can lead to polymer compaction as well as unfolding depending on the strength of polymer-crowder interaction energy. Strongly interacting crowders weaken hydrophobic collapse (or unfold the polymer) at high volume fractions and induce polymer collapse only under dilute conditions. Weakly interacting crowders induce polymer collapse at all crowder concentrations. Interestingly, the thermodynamic driving forces for polymer collapse are remarkably different in the two cases. Strongly and weakly interacting crowders induce collapse by preferential adsorption and preferential depletion respectively. The findings provide new insights into the possible effects of interplay of intermolecular interactions in a crowded environment. The results have implications in understanding the impact of crowding in altering free energy landscapes of proteins.

Pressure, Peptides, and a Piezolyte: Structural Analysis of the Effects of Pressure and Trimethylamine-N-oxide on the Peptide Solvation Shell

The osmolyte trimethylamine-N-oxide (TMAO) is able to increase the thermodynamic stability of folded proteins, counteracting pressure denaturation. Herein, we report experimental solubility data on penta-alanine (pAla) in aqueous TMAO solutions (at pH = 7 and pH = 13) together with molecular simulation data for pAla, penta-serine (pSer), and an elastin-like peptide (ELP) sequence (VPGVG) under varying pH and pressure conditions. The effect of the peptide end groups on TMAO-peptide interactions is investigated by comparing the solvation of zwitterionic and negatively charged pentamers with the solvation of pentamers with charge-neutral C- and N-termini and linear, virtually infinite, peptide chains stretched across the periodic boundaries of the simulation cell. The experiments and simulations consistently show that TMAO is net-depleted from the pAla-water interface, but local accumulation of TMAO is observed just outside the first hydration shell of the peptide. While the same observations are also made in the simulations of the zwitterionic pentamers (Ala, Ser, and ELP) and virtually infinite peptide chains (Ala and ELP), weak preferential binding of TMAO is instead observed for pAla with neutral end groups at a 1 M TMAO concentration and for an ELP pentamer with capped neutral end groups at a 0.55 M TMAO concentration studied in previous work (Y.-T. Liao et al. Proc. Natl. Acad. Sci. USA, 2017, 114, 2479-2484). The above observations made at 1 bar ambient pressure remain qualitatively unchanged at 500 bar and 2 kbar. Local accumulation of TMAO correlates with a reduction in the total number of peptide-solvent hydrogen bonds, independent of the peptide's primary sequence and the applied pressure. By weakening water hydrogen bonds with the protein backbone, TMAO indirectly contributes to stabilizing internal hydrogen bonds in proteins, thus providing a protein stabilization mechanism beyond net depletion.

SJ, van der Vegt NFA. Characterizing Polymer Hydration Shell Compressibilities with the Small-System Method

The small-system method (SSM) exploits the unique feature of finite-sized open systems, whose thermodynamic quantities scale with the inverse system size. This scaling enables the calculation of properties in the thermodynamic limit of macroscopic systems based on computer simulations of finite-sized systems. We herein extend the SSM to characterize the hydration shell compressibility of a generic hydrophobic polymer in water. By systematically increasing the strength of polymer-water repulsion, we find that the excess inverse thermodynamic correction factor (Δ1/Γs∞) and compressibility (Δχs) of the first hydration shell change sign from negative to positive. This occurs with a concurrent decrease in water hydrogen bonding and local tetrahedral order of the hydration shell water. The crossover lengthscale corresponds to an effective polymer bead diameter of 0.7 nm and is consistent with previous works on hydration of small and large hydrophobic solutes. The crossover lengthscale in polymer hydration shell compressibility, herein identified with the SSM approach, relates to hydrophobic interactions and macromolecular conformational equilibria in aqueous solution. The SSM approach may further be applied to study thermodynamic properties of polymer solvation shells in mixed solvents.

(Hyper)Graph Embedding and Classification via Simplicial Complexes

This paper investigates a novel graph embedding procedure based on simplicial complexes. Inherited from algebraic topology, simplicial complexes are collections of increasing-order simplices (e.g., points, lines, triangles, tetrahedrons) which can be interpreted as possibly meaningful substructures (i.e., information granules) on the top of which an embedding space can be built by means of symbolic histograms. In the embedding space, any Euclidean pattern recognition system can be used, possibly equipped with feature selection capabilities in order to select the most informative symbols. The selected symbols can be analysed by field-experts in order to extract further knowledge about the process to be modelled by the learning system, hence the proposed modelling strategy can be considered as a grey-box. The proposed embedding has been tested on thirty benchmark datasets for graph classification and, further, we propose two real-world applications, namely predicting proteins’ enzymatic function and solubility propensity starting from their 3D structure in order to give an example of the knowledge discovery phase which can be carried out starting from the proposed embedding strategy.

Aqueous Mixtures of Urea and Trimethylamine-N-oxide: Evidence for Kosmotropic or Chaotropic Behavior?

Trimethylamine-N-oxide (TMAO) and urea are commonly produced in many extremophilic microorganisms that live in harsh environments. In view of high temperature, high pressure, or high salt content, TMAO is known as a protein structure stabilizer, whereas urea destabilizes protein structures even under ambient conditions. Despite clear evidence, destabilizers are often regarded as chaotropes, meaning water-structure breakers, whereas kosmotropes as water-structure makers are classified as stabilizers. Using atomistic molecular dynamics simulations, we study aqueous mixtures of TMAO and urea in various biologically relevant concentrations to gain insight into the molecular details of their mutual cross-interactions and their influence on water dynamics and structure. Our results for binary and ternary solutions in combination with different mixing ratios show that both co-solutes strengthen the water network in terms of dynamic and structural aspects. Slight differences in the water binding behavior between both species result in only negligible compensation effects. The outcomes of our simulations thus question the validity and the ill-considered use of attributes like kosmotropic or chaotropic substances for stabilizers and destabilizers.