Enthalpic Contributions Research Articles

Nanomaterial Functionalization Modulates Hard Protein Corona Formation: Atomistic Simulations Applied to Graphitic Materials

AbstractThe protein corona is an obstacle to exploiting exotic properties of nanomaterials in clinical and biotechnological settings. The atomic‐scale dynamic formation of the protein corona at the bio‐nano interface is impenetrable using conventional experimental techniques. Here, molecular dynamics simulations are used to study the effect of graphene‐oxide (GO) functionalization on apolipoprotein‐cIII (apo‐c3) adsorption. An analysis pipeline is developed, encompassing binding energy calculations to protein structure analyses employing uniform manifold approximation and projection (UMAP) dimensionality reduction and clustering. It is found that apo‐c3 is denatured by GO adsorption, driven by the large energetic contributions of electrostatic interactions; enthalpic contributions of such binding events outweigh the intraprotein bond enthalpy required to maintain the protein tertiary structure. Through denaturing and exposing buried hydrophobic residues, the protein backbone is stabilized by forming β‐bridges, which serve as binding motifs for protein–protein interactions that drive further protein aggregation on the nanomaterial surface. In contrast, adsorption on double‐clickable azide‐ and alkyne‐double functionalized GO (C2GO), apo‐c3 largely retains its tertiary structure. Binding with the nanomaterial surface is dominated by weaker van der Waals interactions that are dispersed over the protein surface, where charged protein residues are sterically hindered by azide functional groups. The apo‐c3 C‐terminus remains unchanged upon C2GO adsorption, conserving its lipid‐binding function.

The effect of reagents solvation on change in the stability of coordination compounds of silver(I) ion with pyridine in mixed methanol–acetonitrile solvents

In this study, potentiometric titration was used to determine the stability constants of mono- and bis(pyridine) complexes with silver(I) in mixed methanol–acetonitrile solvents. Gibbs free energies of transfer of pyridine from methanol to methanol–acetonitrile mixtures were determined by the method of distribution between two immiscible phases. The effect of solvent composition on change in the solvation state of pyridine was analyzed. The replacement of methanol by acetonitrile leads to the desolvation of pyridine. The resolvation of pyridine occurs predominantly due to the resolvation of the nitrogen atom at the concentration of acetonitrile >0.5 mol fr. The enthalpic contribution was shown to have a major contribution in ΔtrG0(Py)MeOH→(MeOH-AN). The effect of reagents solvation on the stability of [AgPy]+ and [AgPy2]+ complexes upon the change of the solvent composition was investigated. The resolvation of silver(I) was established to be a key factor controlling the stability of both complexes in MeOH-AN mixtures. The possibility of predictive calculation of the stability constants [AgPy]+ in individual and mixed non-aqueous solvents through the change in the Gibbs free energy of the solvation of the complexing ion was shown. Proper data are compared with data reported in the literature.

Cyclic peptides with a distinct arginine-fork motif recognize the HIV trans-activation response RNA in vitro and in cells

RNA represents a potential target for new antiviral therapies, which are urgently needed to address public health threats such as the human immunodeficiency virus (HIV). We showed previously that the interaction between the viral Tat protein and the HIV-1 trans-activation response (TAR) RNA was blocked by TB-CP-6.9a. This cyclic peptide was derived from a TAR-binding loop that emerged during lab evolution of a TAR-binding protein (TBP) family. Here we synthesized and characterized a next-generation, cyclic-peptide library based on the TBP scaffold. We sought to identify conserved RNA-binding interactions and the influence of cyclization linkers on RNA binding and antiviral activity. A diverse group of cyclization linkers, encompassing disulfide bonds to bicyclic aromatic staples, was used to restrain the cyclic peptide geometry. Thermodynamic profiling revealed specific arginine-rich sequences with low to submicromolar affinity driven by enthalpic and entropic contributions. The best compounds exhibited no appreciable off-target binding to related molecules, such as BIV TAR and human 7SK RNAs. A specific arginine-to-lysine change in the highest affinity cyclic peptide reduced TAR binding by tenfold, suggesting that TBP-derived cyclic peptides use an arginine-fork motif to recognize the TAR major groove while differentiating the mode of binding from other TAR-targeting molecules. Finally, we showed that HIV infectivity in cell culture was reduced in the presence of cyclic peptides constrained by methylene or naphthalene-based linkers. Our findings provide insight into the molecular determinants required for HIV-1 TAR recognition and antiviral activity. These findings are broadly relevant to the development of antivirals that target RNA molecules.

Flexible CDOCKER: Hybrid Searching Algorithm and Scoring Function with Side Chain Conformational Entropy.

The binding of small-molecule ligands to protein or nucleic acid targets is important to numerous biological processes. Accurate prediction of the binding modes between a ligand and a macromolecule is of fundamental importance in structure-based structure-function exploration. When multiple ligands with different sizes are docked to a target receptor, it is reasonable to assume that the residues in the binding pocket may adopt alternative conformations upon interacting with the different ligands. In addition, it has been suggested that the entropic contribution to binding can be important. However, only a few attempts to include the side chain conformational entropy upon binding within the application of flexible receptor docking methodology exist. Here, we propose a new physics-based scoring function that includes both enthalpic and entropic contributions upon binding by considering the conformational variability of the flexible side chains within the ensemble of docked poses. We also describe a novel hybrid searching algorithm that combines both molecular dynamics (MD)-based simulated annealing and genetic algorithm crossovers to address the enhanced sampling of the increased search space. We demonstrate improved accuracy in flexible cross-docking experiments compared with rigid cross-docking. We test our developments by considering five protein targets, thrombin, dihydrofolate reductase(DHFR), T4 L99A, T4 L99A/M102Q, and PDE10A, which belong to different enzyme classes with different binding pocket environments, as a representative set of diverse ligands and receptors. Each target contains dozens of different ligands bound to the same binding pocket. We also demonstrate that this flexible docking algorithm may be applicable to RNA docking with a representative riboswitch example. Our findings show significant improvements in top ranking accuracy across this set, with the largest improvement relative to rigid, 23.64%, occurring for ligands binding to DHFR. We then evaluate the ability to identify lead compounds among a large chemical space for the proposed flexible receptor docking algorithm using a subset of the DUD-E containing receptor targets MCR, GCR, and ANDR. We demonstrate that our new algorithms show improved performance in modeling flexible binding site residues compared to DOCK. Finally, we select the T4 L99A and T4 L99A/M102Q decoy sets, containing dozens of binders and experimentally validated nonbinders, to test our approach in distinguishing binders from nonbinders. We illustrate that our new algorithms for searching and scoring have superior performance to rigid receptor CDOCKER as well as AutoDock Vina. Finally, we suggest that flexible CDOCKER is sufficiently fast to be utilized in high-throughput docking screens in the context of hierarchical approaches.

Statistical mechanical model for the formation of octahedral silicon in phosphosilicate glasses

AbstractUnlike ambient pressure silicate glasses, some phosphosilicate glasses contain sixfold‐coordinated silicon (Si6) units even when prepared at ambient pressure. The variation in the fraction of Si6 with composition remains a topic of interest, both for technological applications of phosphosilicate glasses and for fundamental understanding of the glass structure. In this work, we use statistical mechanical modeling to predict the composition–structure relationships in Na2O–P2O5–SiO2 and CaO–P2O5–SiO2 glasses. This is achieved by accounting for the enthalpic and entropic contributions to the interactions between each pairwise modifier ion and structural unit. The initial enthalpy parameters are obtained based on experimental structural data for binary Na2O–SiO2, CaO–SiO2, Na2O–P2O5, and CaO–P2O5 glasses, which can then be transferred to predict the structure of mixed former glasses. This approach has previously been used to predict the short‐range structure of borosilicate and aluminoborate glass systems. However, here we show that the formation of Si6 must be specifically included to make accurate predictions of the composition–structure relationships in phosphosilicate glasses. After incorporating the formation mechanism of Si6 in the statistical mechanics model, we find an excellent agreement between model predictions and experimental structure data for Na2O–P2O5–SiO2 and CaO–P2O5–SiO2 glasses.

Computational Insights into the Aggregation Pathway of Self-Assembled Nanotubules.

We performed molecular dynamics simulations of self-assembled supramolecular nanotubules constructed from amphiphiles with bent-shaped rods. By systematically examining the structure from dimeric aggregates to the fully developed nanotubule, we identified the basic building block of the nanotubule and the optimal dimensions of its stable structure which are consistent with experimental findings. Moreover, we demonstrate that the cooperative interplay of different interactions drives aggregation by selecting and stabilizing the optimal self-assembled structures for various intermediates through a complex pathway. Additionally, contraction of the nanotubule, which accompanies the dehydration process, was observed upon heating. It is suggested that the optimal stability of the self-assembled aggregates is achieved by balancing entropic and enthalpic contributions, of which the ratio is a critical factor that drives the aggregation pathway.

Symmetries in the properties of mixing of AgCu liquid alloys at 1423 K

The quasi-lattice theory based on the joint effect of size ratio and the energetic (or enthalpic) contribution as well as entropic effect has been applied to study the concentration dependence of the thermodynamic and structural properties of AgCu liquid alloys at 1423 K. The analytical expressions for the thermodynamic properties such as excess free energy of mixing, free energy of mixing, entropy of mixing, heat of mixing and the structural properties like the concentration fluctuations in the long wavelength limit and short range order parameter for a binary liquid alloy have been derived in the framework of quasi-lattice theory. The analytical expressions have been used to compute the various thermodynamic and structural properties of liquid AgCu alloys at 1423 K. The theoretical data of thermodynamic and structural properties have been compared with the available experimental data. The present theoretical investigation successfully explains the observed symmetries in the properties of mixing of liquid AgCu alloys at 1423 K.Further the energy parameter is found to be temperature dependent.

Spontaneity of nuclear fusion: a qualitative analysis via classical thermodynamics.

Background: So far the feasibility of nuclear reactions has been studied only through the evaluation of the reaction rate, which gives us information about the kinetics, while the thermodynamic analysis has been limited to evaluations of the change in enthalpy without any consideration of the change in entropy. Methods: This work examines the thermodynamics of nuclear fusion reactions through a simplified approach. The analysis introduces the thermodynamic study of fission and fusion reactions through their comparison with a chemical process. Results: The main result is that fission reactions are always spontaneous (ΔG < 0) since a lot of energy is released in the form of heat and the system moves spontaneously towards a more disordered state. In contrast, fusion reactions are spontaneous only when the enthalpic contribution of the change in Gibbs energy overcomes the entropic contribution. This condition is verified when the temperature of the process is below a characteristic value T*, calculated as the ratio between the energy corresponding to the mass defect and the change of entropy of the fusion reaction. Conclusions: Due to the unavailability of data related to entropy changes in fusion reactions, only a qualitative thermodynamic analysis has been carried out. Through such analysis, the influence of the operating conditions over the spontaneity of fusion processes has been discussed. The final considerations emphasize the role of the thermodynamics analysis that should be implemented in the current studies that, so far, have been mainly based on the assessment of the reaction rate and exothermicity of fusion reactions.

The ubiquitous buried water in the beta-trefoil architecture contributes to the folding nucleus and ~20% of the folding enthalpy.

The beta-trefoil protein architecture is characterized by three repeating "trefoil" motifs related by rotational symmetry and postulated to have evolved via gene duplication and fusion events. Despite this apparent structural symmetry, the primary and secondary structural elements typically exhibit pronounced asymmetric features. A survey of this family of proteins has revealed that among the most conserved symmetric structural elements is a ubiquitous buried solvent which participates in a bridging H-bond with three different beta-strands in each of the trefoil motifs. A computational analysis reported that these waters are likely associated with a substantial enthalpic contribution to overall stability. In this report, a Pro mutation is used to disrupt one of the water H-bond interactions to a main chain amide, and the effects upon stability and folding kinetics are determined. Combined with Ala mutations, the separate effects upon side chain truncation and H-bond deletion are analyzed in terms of stability and folding kinetics. The results show that these buried waters act to assemble a central folding nucleus, and are responsible for ~20% of the overall favorable enthalpy of folding.

Thermodynamics of cytochrome c adsorption on negatively charged gold nanoparticles

In this letter, we have probed the interaction of the heme protein cytochrome c from equine heart (ECc) with negatively charged gold nanoparticles (GNPs) by second harmonic light scattering (SHLS) in solution at pH 10.75 where the protein is also negatively charged. The giant SH response generated from the GNP surface gets quenched due to adsorption of ECc and the isotherm when modelled by a modified Langmuir adsorption model produces the apparent equilibrium binding constant (K), Gibbs free energy change (ΔG) and the maximum number of adsorbed ECc (nsat) on the GNP surface. The thickness of the protein layer on the surface obtained from dynamic light scattering (DLS) experiments show that only monolayer of ECc is formed on the surface and a simple calculation put the fraction of the surface coverage to 0.5 and 0.87 for 41 and 69 nm GNPs, respectively. The enthalpic (ΔH) and entropic (ΔS) contributions to the overall free energy change in adsorption obtained from a temperature dependent SHLS measurement show that the adsorption is primarily driven by enthalpy change indicating the insignificant role played by the electrostatic repulsion between the protein and the GNP surface in the process. Noncovalent interactions seem to dictate the adsorption process while displacement of the water molecules from the surface by the protein molecules do not affect the adsorption process in any major way as evidenced from the measured entropy change.

An ATPase with a twist: A unique mechanism underlies the activity of the bacterial tyrosine kinase, Wzc.

BY-kinases constitute a protein tyrosine kinase family that encodes unique catalytic domains that deviate from those of eukaryotic kinases resembling P-loop nucleotide triphosphatases (NTPases) instead. We have used computational and supporting biochemical approaches using the catalytic domain of the Escherichia coli BY-kinase, Wzc, to illustrate mechanistic divergences between BY-kinases and NTPases despite their deployment of similar catalytic motifs. In NTPases, the “arginine finger” drives the reactive conformation of ATP while also displacing its solvation shell, thereby making favorable enthalpic and entropic contributions toward βγ-bond cleavage. In BY-kinases, the reactive state of ATP is enabled by ATP·Mg2+-induced global conformational transitions coupled to the conformation of the Walker-A lysine. While the BY-kinase arginine finger does promote the desolvation of ATP, it does so indirectly by generating an ordered active site in combination with other structural elements. Bacteria, using these mechanistic variations, have thus repurposed an ancient fold to phosphorylate on tyrosine.

Using a Chromatographic Pseudophase Model To Elucidate the Mechanism of Olefin Separation by Silver(I) Ions in Ionic Liquids.

Silver(I) ions undergo selective olefin complexation and have been utilized in various olefin/paraffin separation techniques such as argentation chromatography and facilitated transport membranes. Ionic liquids (ILs) are solvents known for their low vapor pressure, high thermal stability, low melting points, and ability to promote a favorable solvation environment for silver(I) ion-olefin interactions. To develop highly selective separation systems, a fundamental understanding of analyte partitioning to the stationary phase and the thermodynamic driving forces behind solvation is required. In this study, a chromatographic model treating silver(I) ions as a pseudophase is constructed and employed for the first time to investigate the olefin separation mechanism in silver(I) salt/IL mixtures. Stationary phases containing varying amounts of noncoordinated silver(I) salt ([Ag+][NTf2-]) dissolved in the 1-decyl-3-methylimidazolium bis[(trifluoromethyl)sulfonyl]imide ([C10MIM+][NTf2-]) IL are utilized to determine the partition coefficients of various analytes including alkanes, alkenes, alkynes, aromatics, aldehyde, esters, and ketones. As ligand coordination to silver(I) ions is known to lower its olefin complexation capability, this study also examines two different types of coordinated silver(I) ion pseudophases, namely, monocoordinated silver(I) salt ([Ag+(1-decyl-2-methylimidazole, DMIM)][NTf2-]) and dicoordinated silver(I) salt ([Ag+(1-methylimidazole, MIM)(DMIM)][NTf2-]). The extent of olefin partitioning to the coordinated silver(I) ion pseudophases over the carrier gas and IL decreased by up to two orders of magnitude. Values for enthalpy, entropy, and free energy of solvation were determined for the three silver(I) ion-containing systems. Olefin retention was observed to be enthalpically dominated, while ligand coordination to the silver(I) ion pseudophase resulted in variations for both enthalpic and entropic contributions to the free energy of solvation. The developed model can be used to study chemical changes that occur in silver(I) ions over time as well as identify optimal silver(I) salt/IL mixtures that yield high olefin selectivity.

Influence of Polymer Molecular Weight on Chain Conformation at the Polystyrene/Silver Interface.

The dependence between the conformation of polystyrene (PS) and its molecular weight (Mw) in the vicinity of a metal interface was investigated by sum frequency generation (SFG) spectroscopy. Tilt angles θ ≥ 50° (the angle between the C2 axis of the pendant phenyl ring and the surface normal) were observed for all samples because of the interaction between the aromatic rings and the metal surface. Furthermore, it was found that θ decreases with increasing Mw for PS samples ranging from 20 × 103 g/mol to 400 × 103 g/mol. The intensity of the backbone SFG signal was higher for high Mw PS, compared to low Mw PS, indicating a greater number of backbone interactions with the silver substrate surface for the high Mw sample. These structural differences are driven by different entropic and enthalpic contributions to the free energy of adsorption for different polymer molecular weights. Differences in the polymer free volume and in the relative amount of chain ends with higher mobility may also influence the chain conformation. These results suggest that important interfacial properties of polymeric thin films, such as adhesion and wettability, could be tailored by modifying the polymer Mw to achieve the desired interfacial conformation.

Spontaneity of nuclear fusion: a qualitative analysis via classical thermodynamics

Background: So far the feasibility of nuclear reactions has been studied only through the evaluation of the reaction rate, which gives us information about the kinetics, while the thermodynamic analysis has been limited to evaluations of the change in enthalpy without any consideration of the change in entropy. Methods: This work examines the thermodynamics of nuclear fusion reactions through a simplified approach. The analysis introduces the thermodynamic study of fission and fusion reactions through their comparison with a chemical process. Results: The main result is that fission reactions are always spontaneous (ΔG &lt; 0) since a lot of energy is released in the form of heat and the system moves spontaneously towards a more disordered state. In contrast, fusion reactions are spontaneous only when the enthalpic contribution of the change in Gibbs free energy overcomes the entropic contribution. This condition is verified when the temperature of the process is below a characteristic value T*, calculated as the ratio between the energy corresponding to the mass defect and the change of entropy of the fusion reaction. Conclusions: Due to the unavailability of data related to entropy changes in fusion reactions, only a qualitative thermodynamic analysis has been carried out. Through such analysis, the influence of the operating conditions over the spontaneity of fusion processes has been discussed. The final considerations emphasize the role of the thermodynamics analysis that should be implemented in the current studies that, so far, have been mainly based on the assessment of the reaction rate and exothermicity of fusion reactions.

Aggregate Engineering in Supramolecular Polymers via Extensive Non-covalent Networks

Aggregate engineering of non-covalent networks enables thermo-mechanical versatility of supramolecular polymers, particularly the stimuli-responsive phase transitions and intrinsically damage-healing abilities. However, most non-covalent networks are vulnerable at elevated temperatures, which significantly suppress the robustness of supramolecular polymers. Herein, ureidocytosine (UCy) motifs that can form extensive non-covalent networks and thus robust molecular aggregates via multivalent hydrogen bonds and aromatic stackings, are proposed to enable precise programming of the thermo-mechanical versatility. Molecular simulations reveal that the enthalpic contributions from the UCy aggregates play dominant roles to compensate the entropic loss from the redistributions of polymeric spacers and stabilize the non-covalent networks over wide temperature windows. Such aggregate-level strategy offers prospects for applications which require thermo-mechanical versatility of supramolecular polymers, such as 3D printing, microfabrication and damage-healing coating.

Non-intuitive Trends in Flory–Huggins Interaction Parameters in Polyether-Based Polymers

Recently, a variety of “click” or other additive chemistries have been introduced to functionalize polymers after polymerization to target specific applications, for example, membranes, catalysis, or drug delivery systems. It is generally assumed that the inclusion of these “click” linking groups has minimal impact on the thermodynamics of the polymer as a whole. In this study, we demonstrate that the introduction of these click-derived units has a profound impact on the Flory–Huggins parameter of polyether derivatives. Using random phase approximation fits for small-angle X-ray scattering data from block copolymer pairs to estimate the Flory–Huggins interaction parameter (χ), we determined that poly(ethylene oxide) (PEO) and poly(allyl glycidyl ether) (PAGE), which differ only by the inclusion of an allyl sidechain, have a χ of 0.030 (at T = 34 °C). While PEO is miscible with poly(lactide) (PLA) at nearly all temperatures, the PLA/PAGE χ determined experimentally is 0.015 (at T = 30 °C). Atomistic molecular dynamics simulations of PEO/PAGE oligomer blends show that upon blending, PEO chains contract and move closer together, while PAGE chains stretch and spread apart, indicating an enthalpic contribution to the χ parameter due to changes in polymer coordination resulting from the conformational asymmetry of PAGE and PEO. These studies demonstrate the large impact that functionalization and side-chain units have on the χ parameter of polymer pairs.

Mechanical Properties and Elastic Behavior of Copolymers of Syndiotactic Polypropylene with 1-Hexene and 1-Octene

The mechanical properties of copolymers of syndiotactic polypropylene (sPP) with 1-hexene and 1-octene have been studied and correlated with the structural transformations occurring during stretching and relaxation. These copolymers crystallize in disordered modifications of form I of sPP, with crystallinity, melting, and glass-transition temperatures that decrease with increasing comonomer content. All copolymers show remarkable mechanical properties and elastic behavior, with great improvement of flexibility and ductility with respect to the sPP homopolymer already at small comonomer concentrations. For low comonomer content up to 4–5 mol %, the elastic recovery is associated to a reversible conformational phase transition between the trans-planar form III or the trans-planar mesophase and the helical form II, which gives an enthalpic contribution to the elasticity. As the comonomer content increases, the trans-planar conformation is progressively destabilized and the observed elastic properties are not associated with any conformational transformation during stretching and relaxation. In these cases, copolymers behave as conventional thermoplastic elastomers where elasticity is purely entropic and crystals only act as topological constraints of the elastomeric network. These copolymers represent an exemplary case of the possibility to combine in the same materials desired and apparently incompatible physical properties of elasticity, crystallinity, and strength by controlling the crystallization behavior, achieved by tailoring the chemical structure in the synthetic process.

The enthalpic and entropic terms of the reduction potential of metalloproteins: Determinants and interplay

Splitting the reduction potential of electron transport (ET) proteins and redox metalloenzymes into the enthalpic and entropic contributions is an insightful practice to gaining insight into the molecular determinants of the thermodynamic propensity of the metal center to accept or release electrons. The strict control of such propensity is essential for the functioning of the electron transport chains in bioenergetics and the organized network of the countless reactions of the redox metabolism in all organisms. Here, the first comprehensive overview is offered on the thermodynamic data obtained in the last three decades for the main classes of ET species, namely c-type cytochromes and proteins containing T1 copper and iron-sulfur centers, along with some heme metalloenzymes. These families show many common features in the balance of the enthalpic and entropic terms, which will be brought to light. The enthalpic terms related to ligation features in the first coordination sphere of the metal and weak binding and electrostatics in the surrounding matrix do count a lot in this balance. Reduction entropy is much less important that it would appear from the raw thermodynamic data, particularly for electron transport (ET) metalloproteins. This is due to reduction-induced solvent-related molecular events which dominate the measured entropy changes but affect much less the reduction free energy due to the compensatory effects of the associated enthalpic terms (a phenomenology known as enthalpy-entropy compensation, EEC). Thus the entropy changes seldom exert a real influence on the E°′ of metalloredox proteins; this is restricted to metal sites subjected to reduction-induced protein-based changes in the accessible configurational microstates. It follows that in most cases, especially for ET species, the E° changes due to point mutations, ligand binding and charge changes have an ultimate enthalpic origin. Hence, they should be accounted for with coordination chemistry and electrostatics notions. Only if they don’t, protein-based entropic effects could play a role. In this review, we go through the data gathered for the main classes of ET species and heme enzymes that brought us to this conclusion.

Spontaneity of nuclear fusion: a qualitative analysis via classical thermodynamics

Background: So far the feasibility of nuclear reactions has been studied only through the evaluation of the reaction rate, which gives us information about the kinetics, while the thermodynamic analysis has been limited to evaluations of the change in enthalpy without any consideration of the change in entropy. Methods: This work examines the thermodynamics of nuclear fusion reactions through a simplified approach. The analysis introduces the thermodynamic study of fission and fusion reactions through their comparison with a chemical process. Results: The main result is that fission reactions are always spontaneous (ΔG &lt; 0) since a lot of energy is released in the form of heat and the system moves spontaneously towards a more disordered state. In contrast, fusion reactions are spontaneous only when the enthalpic contribution of the change in Gibbs free energy overcomes the entropic contribution. This condition is verified when the temperature of the process is below a characteristic value T*, calculated as the ratio between the energy corresponding to the mass defect and the change of entropy of the fusion reaction. Conclusions: Due to the unavailability of data related to entropy changes in fusion reactions, only a qualitative thermodynamic analysis has been carried out. Through such analysis, the influence of the operating conditions over the spontaneity of fusion processes has been discussed. The final considerations emphasize the role of the thermodynamics analysis that should be implemented in the current studies that, so far, have been mainly based on the assessment of the reaction rate and exothermicity of fusion reactions.

Spatially resolved free-energy contributions of native fold and molten-globule-like Crambin

The folding stability of a protein is governed by the free-energy difference between its folded and unfolded states, which results from a delicate balance of much larger but almost compensating enthalpic and entropic contributions. The balance can therefore easily be shifted by an external disturbance, such as a mutation of a single amino acid or a change of temperature, in which case the protein unfolds. Effects such as cold denaturation, in which a protein unfolds because of cooling, provide evidence that proteins are strongly stabilized by the solvent entropy contribution to the free-energy balance. However, the molecular mechanisms behind this solvent-driven stability, their quantitative contribution in relation to other free-energy contributions, and how the involved solvent thermodynamics is affected by individual amino acids are largely unclear. Therefore, we addressed these questions using atomistic molecular dynamics simulations of the small protein Crambin in its native fold and a molten-globule-like conformation, which here served as a model for the unfolded state. The free-energy difference between these conformations was decomposed into enthalpic and entropic contributions from the protein and spatially resolved solvent contributions using the nonparametric method Per|Mut. From the spatial resolution, we quantified the local effects on the solvent free-energy difference at each amino acid and identified dependencies of the local enthalpy and entropy on the protein curvature. We identified a strong stabilization of the native fold by almost 500 kJ mol−1 due to the solvent entropy, revealing it as an essential contribution to the total free-energy difference of (53 ± 84) kJ mol−1. Remarkably, more than half of the solvent entropy contribution arose from induced water correlations.