On the molecular mechanism of ion specific Hofmeister series

Hofmeister series ranks the ability of salt ions in influencing a variety of properties and processes in aqueous solutions.In this review,we reexamine how these ions and some other small molecules affect water structure and thermodynamic properties,such as surface tension and protein backbone solvation.We illustrate the difficulties in interpreting the thermodynamic information based on structural and dynamic arguments.As an alternative,we show that the solvation properties of ions and proteins/small molecules can be used to explain the salt effects on the thermodynamic properties of the solutions.Our analysis shows that the often neglected cation-anion cooperativity plays a very important role in these effects.We also argue that the change of hydrogen donor/acceptor equilibrium by added cosolutes/cosolvents can be used to explain their effects on protein secondary structure denaturation/protection:those increase hydrogen donor concentrations such as urea and salts with strongly solvated cations/weakly hydrated anions tend to dissolve protein backbone acting as secondary structure denaturants,whereas those lack of hydrogen donors but rich in acceptors have the opposite effect.     

Entropic barriers in nanoscale adhesion studied by variable temperature chemical force microscopy

Intermolecular interactions drive the vast majority of condensed phase phenomena from molecular recognition to protein folding to particle adhesion. Complex energy barriers encountered in these interactions include contributions from van der Waals forces, hydrogen bonding, and solvent medium. With the spectacular exception of hydrophobic interactions, contributions from the medium are usually considered secondary. We report a variable temperature force microscopy study of the interactions between several hydrogen bonds in different solvents that challenges this point of view. Surprisingly, we observed an increase in the strength of the interaction between carboxylic acid groups in ethanol as the temperature increased. Moreover, when we switched to a nonpolar solvent we observed the opposite behavior: The binding force decreased as the temperature increased. Kinetic model of bond dissociation provided quantitative interpretation of our measurements. We attributed the observed phenomena to a large entropic contribution from the ordered solvent layers that are forming on the probe and sample surfaces upon detachment. The observed reversal in the force vs temperature trend is a manifestation of a transition between thermodynamic and kinetic regimes of unbinding predicted by the model. Our results indicate that entropic barriers dominated by the interactions of solvent molecules with the surface exist in a much wider variety of systems than previously thought.     

Excluded volume entropic effects on protein unfolding times and intermediary stability

The dynamics of protein folding result from both enthalpic and entropic contributions to the free energy. In this paper we focus on entropic volume exclusion effects. We carry out computer simulations using a model that allows us to independently change the size or biochemical properties of amino acid residues. To determine the importance of excluded volume effects, we investigate the effects of changing the size of side chains on the unfolding dynamics of a model four-helix bundle protein. In addition, we also investigate the effects of changing the thickness of the chain's backbone. This has relevance to the behavior of synthetic polymers where the size of the constituent units can be varied. We find that entropic excluded volume effects are crucially important for stabilizing the organized native state relative to the molten globule.     

Rheology of foams and highly concentrated emulsions

We review the state of the art in foam and highly concentrated emulsion rheology, with an emphasis on progress made over the last five years. Since the structures and physico-chemical processes relevant for foams and emulsions are closely analogous, comparing the knowledge recently gained in these two neighboring fields brings fresh insight. In this spirit, we review how the macroscopic mechanical response arises from a coupling between interfacial energy and long range molecular interactions, entropic effects, interfacial rheology, and dynamics at the droplet or bubble scale. We present experiments and models concerning elasticity, osmotic pressure, yielding and flow behavior.     

Analytical model for studying how environmental factors influence protein conformational stability in solution

We introduce an analytical modeling strategy for probing the conformational stability of globular proteins in aqueous solution. In this approach, the intrinsic (i.e., infinite dilution) thermodynamic stability and coarse structural properties of the proteins, as well as the effective protein-protein interactions, derive from a heteropolymer collapse theory that incorporates predicted temperature- and pressure-dependent hydrophobic interactions. Protein concentration effects are estimated by integrating this information into a molecular thermodynamic model, which is an ad hoc generalization of the exact equilibrium theory of a one-dimensional binary mixture of square-well particles that interconvert through an isomerization (i.e., folding) reaction. The end result is an analytical multiscale modeling approach which, although still schematic, can predict that folded proteins exhibit a closed-loop region of stability in the pressure-temperature plane and that protein concentration has a nonmonotonic effect on protein stability, results consistent with qualitative trends observed in both experiments of protein solutions and simulations of coarse-grained protein models.     

Lattice model of oligonucleotide hybridization in solution. I. Model and thermodynamics

A coarse-grained lattice model of DNA oligonucleotides is proposed to investigate the general mechanisms by which single-stranded oligonucleotides hybridize to their complementary strands in solution. The model, based on a high-coordination cubic lattice, is simple enough to allow the direct simulation of DNA solutions, yet capturing how the fundamental thermodynamic processes are microscopically encoded in the nucleobase sequences. Physically relevant interactions are considered explicitly, such as interchain excluded volume, anisotropic base-pairing and base-stacking, and single-stranded bending rigidity. The model is studied in detail by a specially adapted Monte Carlo simulation method, based on parallel tempering and biased trials, which is designed to overcome the entropic and enthalpic barriers associated with the sampling of hybridization events of multiple single-stranded chains in solution. This methodology addresses both the configurational complexity of bringing together two complementary strands in a favorable orientation (entropic barrier) and the energetic penalty of breaking apart multiple associated bases in a double-stranded state (enthalpic barrier). For strands with sequences restricted to nonstaggering association and homogeneous pairing and stacking energies, base-pairing is found to dominate the hybridization over the translational and conformational entropy. For strands with sequence-dependent pairing corresponding to that of DNA, the complex dependence of the model's thermal stability on concentration, sequence, and degree of complementarity is shown to be qualitatively and quantitatively consistent both with experiment and with the predictions of statistical mechanical models.     

A semi-analytical description of protein folding that incorporates detailed geometrical information

Much has been done to study the interplay between geometric and energetic effects on the protein folding energy landscape. Numerical techniques such as molecular dynamics simulations are able to maintain a precise geometrical representation of the protein. Analytical approaches, however, often focus on the energetic aspects of folding, including geometrical information only in an average way. Here, we investigate a semi-analytical expression of folding that explicitly includes geometrical effects. We consider a Hamiltonian corresponding to a Gaussian filament with structure-based interactions. The model captures local features of protein folding often averaged over by mean-field theories, for example, loop contact formation and excluded volume. We explore the thermodynamics and folding mechanisms of beta-hairpin and alpha-helical structures as functions of temperature and Q, the fraction of native contacts formed. Excluded volume is shown to be an important component of a protein Hamiltonian, since it both dominates the cooperativity of the folding transition and alters folding mechanisms. Understanding geometrical effects in analytical formulae will help illuminate the consequences of the approximations required for the study of larger proteins.     

From Valleys to Ridges: Exploring the Dynamic Energy Landscape of Single Membrane Proteins

Membrane proteins are involved in essential biological processes such as energy conversion, signal transduction, solute transport and secretion. All biological processes, also those involving membrane proteins, are steered by molecular interactions. Molecular interactions guide the folding and stability of membrane proteins, determine their assembly, switch their functional states or mediate signal transduction. The sequential steps of molecular interactions driving these processes can be described by dynamic energy landscapes. The conceptual energy landscape allows to follow the complex reaction pathways of membrane proteins while its modifications describe why and how pathways are changed. Single‐molecule force spectroscopy (SMFS) detects, quantifies and locates interactions within and between membrane proteins. SMFS helps to determine how these interactions change with temperature, point mutations, oligomerization and the functional states of membrane proteins. Applied in different modes, SMFS explores the co‐existence and population of reaction pathways in the energy landscape of the protein and thus reveals detailed insights into local mechanisms, determining its structural and functional relationships. Here we review how SMFS extracts the defining parameters of an energy landscape such as the barrier position, reaction kinetics and roughness with high precision.     

Surface Attachment Enhances the Thermodynamic Stability of Protein L

Despite the importance of protein–surface interactions in both biology and biotechnology, our understanding of their origins is limited due to a paucity of experimental studies of the thermodynamics behind such interactions. In response, we have characterized the extent to which interaction with a chemically well‐defined macroscopic surface alters the stability of protein L. To do so, we site‐specifically attached a redox‐reporter‐modified protein variant to a hydroxy‐terminated monolayer on a gold surface and then used electrochemistry to monitor its guanidine denaturation and determine its folding free energy. Comparison with the free energy seen in solution indicates that interaction with this surface stabilizes the protein by 6 kJ mol^?1, a value that is in good agreement with theoretical estimates of the entropic consequences of surface‐induced excluded volume effects, thus suggesting that chemically specific interactions with this surface (e.g., electrostatic interactions) are limited in magnitude.     

Dissecting entropic coiling and poor solvent effects in protein collapse

The early events in protein collapse and folding are guided by the protein's elasticity. The contributions of entropic coiling and poor solvent effects like hydrophobic forces to the elastic response of proteins are currently unknown. Using molecular simulations of stretched ubiquitin in comparison with models of proteins as entropic chains, we find a surprisingly high stiffness of the protein backbone, reflected by a persistence length of 1.2 nm, which is significantly reduced by hydrophobic forces acting between protein side chains to an apparent persistence length of 0.3-0.6 nm frequently observed in single-molecule stretching experiments. Thus, the poor solvent conditions of a protein in water lead to a protein compaction much beyond the coiling of an entropic chain and thereby allow a protein to appear softer than when using good solvents.     

Comparative adsorption studies of indigo carmine dye on chitin and chitosan

The adsorption of indigo carmine dye onto chitin and chitosan from aqueous solutions was followed in a batch system. The ability of these materials to adsorb indigo carmine dye from aqueous solution was followed through a series of adsorption isotherms adjusted to a modified Langmuir equation. The maximum number of moles adsorbed was 1.24 +/- 0.16 x 10(-5) and 1.54 +/- 0.03 x 10(-4) mol g(-1) for chitin and chitosan, respectively. The same interactions were calorimetrically followed and the thermodynamic data showed exothermic enthalpic values of -40.12 +/- 3.52 and -29.25 +/- 1.93 kJ mol(-1) for chitin and chitosan, respectively. Gibbs free energies for the two adsorption processes of indigo carmine dye presented a positive value for chitin and a negative one for chitosan, reflecting that dye/surface interactions are thermodynamic favorable for chitosan and nonspontaneous for chitin at 298.15 K. The interaction processes were accompanied by an increase of entropy value for chitosan (90 +/- 6 J mol(-1)K(-1)) and a decrease for chitin (-145 +/- 13 J mol(-1)K(-1)). Thus, dye/chitosan interaction showed favorable enthalpic and entropic processes, reflecting thermodynamic stability of the formed complex, while dye/chitin interaction showed an exothermic enthalpic value and a highly nonfavorable entropic effect, resulting in a nonspontaneous thermodynamic system.     

Effect of Molecular Crowding on the Temperature–Pressure Stability Diagram of Ribonuclease A

FT‐IR spectroscopic and thermodynamic measurements were designed to explore the effect of a macromolecular crowder, dextran, on the temperature and pressure‐dependent phase diagram of the protein Ribonuclease A (RNase A), and we compare the experimental data with approximate theoretical predictions based on configuration entropy. Exploring the crowding effect on the pressure‐induced unfolding of proteins provides insight in protein stability and folding under cell‐like dense conditions, since pressure is a fundamental thermodynamic variable linked to molecular volume. Moreover, these studies are of relevance for understanding protein stability in deep‐sea organisms, which have to cope with pressures in the kbar range. We found that not only temperature‐induced equilibrium unfolding of RNase A, but also unfolding induced by pressure is markedly prohibited in the crowded dextran solutions, suggesting that crowded environments such as those found intracellularly, will also oppress high‐pressure protein unfolding. The FT‐IR spectroscopic measurements revealed a marked increase in unfolding pressure of 2 kbar in the presence of 30 wt % dextran. Whereas the structural changes upon thermal unfolding of the protein are not significantly influenced in the presence of the crowding agent, through stabilization by dextran the pressure‐unfolded state of the protein retains more ordered secondary structure elements, which seems to be a manifestation of the entropic destabilization of the unfolded state by crowding.     

Thermodynamic basis for promiscuity and selectivity in protein-protein interactions: PDZ domains, a case study

Like other protein-protein interaction domains, PDZ domains are involved in many key cellular processes. These processes often require that specific multiprotein complexes be assembled, a task that PDZ domains accomplish by binding to specific peptide motifs in target proteins. However, a growing number of experimental studies show that PDZ domains (like other protein-protein interaction domains) can engage in a variety of interactions and bind distinct peptide motifs. Such promiscuity in ligand recognition raises intriguing questions about the molecular and thermodynamic mechanisms that can sustain it. To identify possible sources of promiscuity and selectivity underlying PDZ domain interactions, we performed molecular dynamics simulations of 20 to 25 ns on a set of 12 different PDZ domain complexes (for the proteins PSD-95, Syntenin, Erbin, GRIP, NHERF, Inad, Dishevelled, and Shank). The electrostatic, nonpolar, and configurational entropy binding contributions were evaluated using the MM/PBSA method combined with a quasi-harmonic analysis. The results revealed that PDZ domain interactions are characterized by overwhelmingly favorable nonpolar contributions and almost negligible electrostatic components, a mix that may readily sustain promiscuity. In addition, despite the structural similarity in fold and in recognition modes, the entropic and other dynamical aspects of binding were remarkably variable not only across PDZ domains but also for the same PDZ domain bound to distinct ligands. This variability suggests that entropic and dynamical components can play a role in determining selectivity either of PDZ domain interactions with peptide ligands or of PDZ domain complexes with downstream effectors.     

Exploiting Large‐Pore Metal–Organic Frameworks for Separations through Entropic Molecular Mechanisms

We review the molecular mechanisms behind adsorption and the separations of mixtures in metal–organic frameworks and zeolites. Separation mechanisms can be based on differences in the affinity of the adsorbate with the framework and on entropic effects. To develop next‐generation adsorbents, the separation efficiency of the materials needs to be improved. The performance under industrially relevant conditions largely depends on two factors: 1) the separation selectivity and 2) the pore volume capacity of the material. Enthalpic mechanisms can lead to increased selectivities, but these are mostly restricted to the low loading regime, and hence these mechanisms are unable to make use of all of the large‐pore volume that a metal–organic framework can provide. Industrial processes routinely operate in the pore saturation regime. In this Review, we focus on entropic molecular separation mechanisms that are effective under these conditions and, in particular, on a recent methodology to obtain high selectivities at high pore loading.     

Understanding thermodynamic competitivity between biopolymer folding and misfolding under large-scale intermolecular interactions

Cooperativity is a hallmark of spontaneous biopolymer folding. The presence of intermolecular interactions could create off-pathway misfolding structures and suppress folding cooperativity. This raises the hypothesis that thermodynamic competitivity between off-pathway misfolding and on-pathway folding may intervene with cooperativity and govern biopolymer folding dynamics under conditions permitting large-scale intermolecular interactions. Here we report direct imaging and theoretical modeling of thermodynamic competitivity between biopolymer folding and misfolding under such conditions, using a two-dimensional array of proton-fueled DNA molecular motors packed at the maximal density as a model system. Time-resolved liquid-phase atomic force microscopy with enhanced phase contrast revealed that the misfolding and folding intermediates transiently self-organize into spatiotemporal patterns on the nanoscale in thermodynamic states far away from equilibrium as a result of thermodynamic competitivity. Computer simulations using a novel cellular-automaton network model provide quantitative insights into how large-scale intermolecular interactions correlate the structural dynamics of individual biomolecules together at the systems level.     

Tightening up the structure,lighting up the pathway: application of molecular constraints and light to manipulate protein folding,self-assembly and function

Chemical cross-linking provides an effective avenue to reduce the conformational entropy of polypeptide chains and hence has become a popular method to induce or force structural formation in peptides and proteins.Recently,other types of molecular constraints,especially photoresponsive linkers and functional groups,have also found increased use in a wide variety of applications.Herein,we provide a concise review of using various forms of molecular strategies to constrain proteins,thereby stabilizing their native states,gaining insight into their folding mechanisms,and/or providing a handle to trigger a conformational process of interest with light.The applications discussed here cover a wide range of topics,ranging from delineating the details of the protein folding energy landscape to controlling protein assembly and function.     

Macromolecular compaction by mixed solutions: Bridging versus depletion attraction

From colloidal dispersions to solvated polymers or proteins, solution composition is known to strongly influence the stable state of the bathing macromolecules. Mixed solvents containing species with different affinities to specific macromolecular states can shift equilibrium towards the thermodynamically preferred state with lower free energy, even when the molecular interactions with the solvent are weak. We review two known mechanisms, bridging and depletion attraction, and discuss how each can emerge, depending on the molecular size and interaction of the mixed solvent species. We show that simple theoretical considerations predict that the macromolecular state that is stabilized by each mechanism possesses unique structural properties, as well as distinct thermodynamic fingerprints. Furthermore, we demonstrate the mechanistic role of enthalpy and entropy, as seen in a simple mean field model of macromolecules in mixed solvents. These thermodynamic contributions determine the temperature dependence of cosolute induced effects. Finally, we review the possible role of fluctuations, and point to possible implications and open questions.