Origin of heat capacity changes in a "nonclassical" hydrophobic interaction

Methyl•••Methyl Interactions in Proteins: Insights from Structural and Computational Studies

The low affinity of nonpolar groups for water gave birth to one of the significant supramolecular forces known as hydrophobic interaction as early as 1937. While the precise origins of this phenomenon remain debated, the significant role of London dispersion forces in stabilizing nonpolar complexes is well-established. This article presents a comprehensive investigation of the nature and strength of CH3•••H3C (methyl-methyl) interactions within the amino acid residues of proteins, employing a combination of quantum mechanical calculations and custom Python code. Analysis of isolated mimetic dipeptide models reveals that these interactions are weak, with interaction energies ranging from -2.40 to -6.94 kJ/mol. These energies are primarily attributed to dispersion forces, supplemented by a minor electrostatic contribution. Even though CH3•••H3C interactions are weak, the cumulative effect of such interactions is vital for the flexible enzymatic center and drug-protein interactions. Although experimental characterization of these weak interactions is challenging, our computational studies, presented herein, suggest that solution-phase 13C NMR and the recently developed gas-phase terahertz (THz) spectroscopy offer promising avenues for obtaining spectroscopic signatures of CH3•••H3C interactions and elucidating their strength and molecular origin.

Cyclodextrin Derivatives as Modulators for Enhanced Drug Delivery from Niosome Membrane: A Fluorescence Correlation Spectroscopy and Isothermal Titration Calorimetry Approach

Designing efficient drug delivery systems for optimum therapeutic outcomes and minimum adverse effects remains a pivotal focus in pharmaceutical research. Understanding the nature of interactions between drugs and drug carriers and the drug-release mechanism are the key aspects for the development of effective delivery systems. This work presents a detailed investigation into the intricate interactions between niosomes and the drug Phenosafranin (PSF), and the subsequent release induced by a variety of cyclodextrins (CDs) employing a multifaceted approach. Ensemble average spectroscopic and single molecular level investigations based on fluorescence correlation spectroscopy (FCS), are employed to explore the binding interactions of PSF with the niosome membrane. Subsequently, the release of the drug was studied by disrupting the niosome structure using various CDs, and their efficacy was accessed through steady-state and time-resolved photophysical responses. FCS experiments provided precise insights into the binding and drug release process at the single-molecule level through the variation in translational and diffusion characteristics of the drug. Additionally, isothermal titration calorimetric (ITC) investigations further revealed the thermodynamics governing the CD-niosome host:guest interactions and the varying potential of different CDs in disrupting the niosome to release the drug which were further validated by electron microscopy and confocal fluorescence microscopy analyses. A broader analysis of niosomes prepared with various nonionic surfactants highlighted the influence of cavitand size and structure on the interaction with different niosome constituents. This comprehensive analysis sheds light on the complex interplay of these components and their interactions, providing insights into drug delivery systems and their potential therapeutic applications.

Distinction and Quantification of Noncovalent Dispersive and Hydrophobic Effects

The possibilities of comparing computational results of noncovalent interactions with experimental data are discussed, first with respect to intramolecular interactions. For these a variety of experimental data such as heats of formation, crystal sublimation heats, comparison with energy minimized structures, and spectroscopic data are available, but until now largely have not found widespread application. Early force field and QM/MP2 calculations have already shown that the sublimation heats of hydrocarbons can be predicted with an accuracy of ±1%. Intermolecular interactions in solution or the gas phase are always accompanied by difficult to compute entropic contributions, like all associations between molecules. Experimentally observed T∆S values contribute 10% to 80% of the total ∆G, depending on interaction mechanisms within the complexes, such as, e.g., hydrogen bonding and ion pairing. Free energies ∆G derived from equilibrium measurements in solution allow us to define binding increments ∆∆G, which are additive and transferable to a variety of supramolecular complexes. Data from more than 90 equilibrium measurements of porphyrin receptors in water indicate that small alkanes do not bind to the hydrophobic flat surfaces within a measuring limit of ∆G = ±0.5 kJ/mol, and that 20 functions bearing heteroatoms show associations by dispersive interactions with up to ∆G = 8 kJ/mol, roughly as a function of their polarizability. Aromatic systems display size-dependent affinities ∆G as a linear function of the number of π-electrons.

The temperature-dependence of host-guest binding thermodynamics: experimental and simulation studies

The thermodynamic parameters of host-guest binding can be used to describe, understand, and predict molecular recognition events in aqueous systems. However, interpreting binding thermodynamics remains challenging, even for these relatively simple molecules, as they are determined by both direct and solvent-mediated host-guest interactions. In this contribution, we focus on the contributions of water to binding by studying binding thermodynamics, both experimentally and computationally, for a series of nearly rigid, electrically neutral host-guest systems and report the temperature-dependent thermodynamic binding contributions ΔGb(T), ΔHb(T), ΔSb(T), and ΔCp,b. Combining isothermal titration calorimetry (ITC) measurements with molecular dynamics (MD) simulations, we provide insight into the binding forces at play for the macrocyclic hosts cucurbit[n]uril (CBn, n = 7-8) and β-cyclodextrin (β-CD) with a range of guest molecules. We find consistently negative changes in heat capacity on binding (ΔCp,b) for all systems studied herein - as well as for literature host-guest systems - indicating increased enthalpic driving forces for binding at higher temperatures. We ascribe these trends to solvation effects, as the solvent properties of water deteriorate as temperature rises. Unlike the entropic and enthalpic contributions to binding, with their differing signs and magnitudes for the classical and non-classical hydrophobic effect, heat capacity changes appear to be a unifying and more general feature of host-guest complex formation in water. This work has implications for understanding protein-ligand interactions and other complex systems in aqueous environments.

The role of hydrophobic interactions in the molten globule state of globular protein modulated by surfactants

In order to highlight the role of hydrophobic interactions in the molten globule (MG) state of globular protein modulated by surfactants, the interactions of bovine α-lactalbumin (α-LA) with alkyl trimethylammonium bromides (CnTAB, n = 10, 12, 14, and 16) have been studied by experimental and theoretical techniques. Isothermal titration calorimetry (ITC) showed that the enthalpy changes (ΔH) and area of the enthalpogram increased with increasing the chain length of CnTAB. The result of fluorescence, circular dichroism (CD) and 1H nuclear magnetic resonance (NMR) spectrum suggested that C10TAB and C12TAB unfolded α-LA partially, C14TAB reconstructed protein with a native-like secondary structure content, and C16TAB induced an MG state α-LA. The SAXS results confirmed that the tertiary structure of α-LA was disrupted by C16TAB forming an MG state complex with a micelle-like structure even at the surfactants concentrations below CMC. As indicated by MD results, the β-domain and unstructured region(s) were involved in the MG state α-LA modulated by CnTAB. This work not only provides molecular insights into the role of hydrophobic interactions in the MG state of a globular protein but also helps understand the mechanism of preparing α-LA based biomacromolecule modulated by hydrophobic interactions.

Binding Thermodynamics and Interaction Patterns of Inhibitor-Major Urinary Protein-I Binding from Extensive Free-Energy Calculations: Benchmarking AMBER Force Fields

Mouse major urinary protein (MUP) plays a key role in the pheromone communication system. The one-end-closed β-barrel of MUP-I forms a small, deep, and hydrophobic central cavity, which could accommodate structurally diverse ligands. Previous computational studies employed old protein force fields and short simulation times to determine the binding thermodynamics or investigated only a small number of structurally similar ligands, which resulted in sampled regions far from the experimental structure, nonconverged sampling outcomes, and limited understanding of the possible interaction patterns that the cavity could produce. In this work, extensive end-point and alchemical free-energy calculations with advanced protein force fields were performed to determine the binding thermodynamics of a series of MUP-inhibitor systems and investigate the inter- and intramolecular interaction patterns. Three series of inhibitors with a total of 14 ligands were simulated. We independently simulated the MUP-inhibitor complexes under two advanced AMBER force fields. Our benchmark test showed that the advanced AMBER force fields including AMBER19SB and AMBER14SB provided better descriptions of the system, and the backbone root-mean-square deviation (RMSD) was significantly lowered compared with previous computational studies with old protein force fields. Surprisingly, although the latest AMBER force field AMBER19SB provided better descriptions of various observables, it neither improved the binding thermodynamics nor lowered the backbone RMSD compared with the previously proposed and widely used AMBER14SB. The older but widely used AMBER14SB actually achieved better performance in the prediction of binding affinities from the alchemical and end-point free-energy calculations. We further analyzed the protein-ligand interaction networks to identify important residues stabilizing the bound structure. Six residues including PHE38, LEU40, PHE90, ALA103, LEU105, and TYR120 were found to contribute the most significant part of protein-ligand interactions, and 10 residues were found to provide favorable interactions stabilizing the bound state. The two AMBER force fields gave extremely similar interaction networks, and the secondary structures also showed similar behavior. Thus, the intra- and intermolecular interaction networks described with the two AMBER force fields are similar. Therefore, AMBER14SB could still be the default option in free-energy calculations to achieve highly accurate binding thermodynamics and interaction patterns.

Characterization of Octreotide-PLGA Binding by Isothermal Titration Calorimetry

Cationic peptides are well known to readily bind poly(lactic-co-glycolic acids) (PLGAs) with a carboxylic acid (-COOH) end group, which poses a significant challenge to develop PLGA-based delivery systems for peptide therapeutics. This binding has been considered as a critical step leading to the peptide acylation within PLGA-based formulations, which is also known to affect microencapsulation and release. Herein, we utilized nano isothermal titration calorimetry (NanoITC) to investigate the thermodynamics of peptide-PLGA binding in dimethyl sulfoxide (DMSO) using a model cationic octapeptide, octreotide, which contains two primary amino groups located at its N-terminus and lysine side chain at position five. ITC results of PLGAs with different lactic acid to glycolic acid ratios (50:50 to 100:0) revealed that the extent of the interaction with the octreotide was solely dependent on the availability of the acid end group of the PLGA. The binding constants (K_a) at 37 °C were determined in a narrow range from 1.33 to 1.72 × 10⁴ M^-1 with 0.59 to 0.66 binding stoichiometries irrespective of the lactic/glycolic acid ratio in the PLGA-COOH. Over 25-65 °C, the octreotide-PLGA-COOH interactions were found to be enthalpically favored (ΔH < 0) and entropically unfavorable (ΔS < 0). Hence, the interactions were characterized as enthalpically driven. At different sodium chloride (NaCl) levels, the sensitivity of thermodynamics of the interactions to the charge screening effect contributed by the NaCl unveiled the actual driving force of the octreotide-PLGA-COOH interactions is simple ion-pairing.

The study of EGFR-ligand complex electron property relationship with biological activity

The present investigation grounded on estimation of electron properties of the structures of EGFR proteins-ligand complexes using our laboratory-developed methodology AlteQ approach, which describes the molecular electron density of the complex in space for a certain point in three-dimensional coordinates. Briefly, the system embodies molecular electron density as a sum of Slater's type atomic increments of the molecular system. Further, using this methodology, we calculated different electron characteristics of selected EGFR protein-ligand complexes and established the relationship between different electron properties with their experimental pharmacological activity value (pIC₅₀). The study suggested that EGFR inhibitory activity has higher correlation with intermolecular contacts of H with pi-system of aromatic ring between protein and ligands. Therefore, this created model has impact to identify and design potential ligands against EGFR in anticancer drug discovery.Communicated by Ramaswamy H. Sarma.

Contrasting Thermodynamics Governs the Interaction of 3-Hydroxyflavone with the N-Isoform and B-Isoform of Human Serum Albumin

Herein we report the interaction of 3-hydroxyflavone (3HF) with various isomeric forms of Human Serum Albumin (HSA), namely, the N-isoform (or native HSA at pH 7.4) and the B-isoform (at pH 9.2). Spectroscopic signatures of 3HF reveal that the interaction of 3HF with the N-isoform of HSA results in significant lowering of absorbance of the neutral species (λ_abs ∼ 345 nm) with concomitant increase of the anionic species (λ_abs ∼ 416 nm) whereas interaction with the B-isoform of HSA leads to selective enhancement of absorbance of the anionic species. The fluorescence profile of 3HF displays marked increase of intensity of the proton transferred tautomer (λ_em ∼ 538 nm) as well as the anionic species (λ_em ∼ 501 nm) for both the forms of the protein. However, analyses of the associated thermodynamics through temperature-dependent isothermal titration calorimetric (ITC) indicate that the interaction of 3HF with the N-isoform of HSA is more enthalpic in the lower temperature limit while the entropy contribution predominates in the higher temperature limit. Consequently, the 3HF-HSA (N-isoform at pH 7.4) interaction reveals an unusual thermodynamic signature of a positive heat capacity change (ΔC_p = 3.84 kJ mol^-1K^-1) suggesting the instrumental role of hydrophobic hydration. On the contrary, the 3HF-HSA (B-isoform at pH 9.2) interaction shows qualitatively reverse effect. Consequently, the interaction is found to be characterized by an enthalpy-dominated hydrophobic effect (negative heat capacity change, ΔC_p = -1.15 kJ mol^-1K^-1) which is rationalized on the basis of the nonclassical hydrophobic effect.

Estimation of a stronger heparin binding locus in fibronectin domain III14using thermodynamics and molecular dynamics

The HEP II (Heparin-binding site II) region of fibronectin (FN) containing domain III¹⁴ plays a crucial role in cell adhesion and migration through heparin-binding on the cell surface. There are two such fibronectin heparin interacting peptide (FHIP I and FHIP II) sequences present in HEP II. However, the molecular principles by which these sites orchestrate heparin-binding processes are poorly understood. Such knowledge would have great implications in the therapeutic targeting of FN. With this aim, we have explored the binding studies of FHIP I and FHIP II with heparin using various biophysical methods. A fluorescence melting study specifically revealed the preference of heparin for domain III in FN, indicating the key contribution of FHIP I and FHIP II in heparin binding. In isothermal titration calorimetry (ITC), the higher binding affinity observed for FHIP II (∼10⁷ mol⁻¹) compared to FHIP I (∼10⁶ mol⁻¹) is expected due to the presence of a superior cluster of Arg and Lys residues in FHIP II, which can facilitate specific H-bonding interactions with heparin. Based on heat capacity changes, the key role of H-bonding, electrostatic and hydrophobic interactions was demonstrated in binding. Finally, the molecular docking and MD simulation results reinforced that the interaction of heparin (dodecasaccharide) is stronger and stable with the FHIP II peptide. The results described here suggest that these peptides provide all the structural and thermodynamic elements necessary for heparin-binding of HEP II of FN. Subsequently, it can be concluded that FHIP II could be a better location for therapeutic intervention in cell adhesion activity by FN.

Binding Thermodynamics of FHIP I and FHIP II with heparin.

Effect of Photoacid Strength on Fluorescence Modulation of 2-Naphthol Derivatives inside β-Cyclodextrin Cavity: Insights from Fluorescence, Isothermal Calorimetry, and Molecular Dynamics Simulations

Fluorescence response of a photoacid inside a confined environment often differs markedly from the bulk response. Is there any correlation between the extent of fluorescence modulation and the strength of the photoacid? Here, we used three photoacids: 2-naphthol (2OH, pK_a* = 3.3), 6-sulfonate-2-naphthol (6SO₃-2OH, pK_a* = 3.06), and 6-cyano-2-naphthol (6CN-2OH, pK_a* = 0.6) with remarkably different excited-state acidities to investigate fluorescence modulation inside the nanocavity of β-cyclodextrin (β-CD). Interestingly, we found strong fluorescence modulation for 2OH and 6SO₃-2OH but almost none for 6CN-2OH. Isothermal calorimetry measurements showed that all three fluorophores form 1:1 inclusion complex with comparable binding constants (285, 420, and 580 M^-1 for 2OH, 6SO₃-2OH, and 6CN-2OH, respectively). Molecular dynamics simulation further revealed that binding modes are quite similar, and the distribution of water molecules around the proton-donating hydroxyl group of the photoacids are also comparable. Consequently, the difference in the fluorescence response should be accounted solely to the difference in the photoacidity strengths.

The Molecular Origin of Enthalpy/Entropy Compensation in Biomolecular Recognition

Biomolecular recognition can be stubborn; changes in the structures of associating molecules, or the environments in which they associate, often yield compensating changes in enthalpies and entropies of binding and no net change in affinities. This phenomenon—termed enthalpy/entropy (H/S) compensation—hinders efforts in biomolecular design, and its incidence—often a surprise to experimentalists—makes interactions between biomolecules difficult to predict. Although characterizing H/S compensation requires experimental care, it is unquestionably a real phenomenon that has, from an engineering perspective, useful physical origins. Studying H/S compensation can help illuminate the still-murky roles of water and dynamics in biomolecular recognition and self-assembly. This review summarizes known sources of H/ S compensation (real and perceived) and lays out a conceptual framework for understanding and dissecting—and, perhaps, avoiding or exploiting—this phenomenon in biophysical systems.

Amphiphiles without Head-and-Tail Design: Nanostructures Based on the Self-Assembly of Anionic Boron Cluster Compounds

Anionic boron cluster compounds (ABCCs) are intrinsically amphiphilic building blocks suitable for nanochemistry. ABCCs are involved in atypical weak interactions, notably dihydrogen bonding, due to their peculiar polyhedral structure, consisting of negatively charged B-H units. The most striking feature of ABCCs that differentiates them from typical surfactants is the lack of head-and-tail structure. Furthermore, their structure can be described as intrinsically amphiphilic or aquaneutral. Therefore, classical terms established to describe self-assembly of classical amphiphiles are insufficient and need to be reconsidered. The opinions and theories focused on the solution behavior of ABCCs are briefly discussed. Moreover, a comparison between ABCCs with other amphiphilic systems is made focusing on the explanation of enthalpy-driven micellization or relations between hydrophobic and chaotropic effects. Despite the unusual structure, ABCCs still show self- and coassembly properties comparable to classical amphiphiles such as ionic surfactants. They self-assemble into micelles in water according to the closed association model. The most typical features of ABCCs solution behavior is demonstrated on calorimetry, NMR spectroscopy, and tensiometry experiments. Altogether, the unique features of ABCCs makes them a valuable inclusion into the nanochemisty toolbox to develop novel nanostructures both alone and with other molecules.

Molecular Shape and the Hydrophobic Effect

This review focuses on papers published since 2000 on the topic of the properties of solutes in water. More specifically, it evaluates the state of the art of our understanding of the complex relationship between the shape of a hydrophobe and the hydrophobic effect. To highlight this, we present a selection of references covering both empirical and molecular dynamics studies of small (molecular-scale) solutes. These include empirical studies of small molecules, synthetic hosts, crystalline monolayers, and proteins, as well as in silico investigations of entities such as idealized hard and soft spheres, small solutes, hydrophobic plates, artificial concavity, molecular hosts, carbon nanotubes and spheres, and proteins.

Stealth Amphiphiles: Self-Assembly of Polyhedral Boron Clusters

This is the first experimental evidence that both self-assembly and surface activity are common features of all water-soluble boron cluster compounds. The solution behavior of anionic polyhedral boranes (sodium decaborate, sodium dodecaborate, and sodium mercaptododecaborate), carboranes (potassium 1-carba-dodecaborate), and metallacarboranes {sodium [cobalt bis(1,2-dicarbollide)]} was extensively studied, and it is evident that all the anionic boron clusters form multimolecular aggregates in water. However, the mechanism of aggregation is dependent on size and polarity. The series of studied clusters spans from a small hydrophilic decaborate-resembling hydrotrope to a bulky hydrophobic cobalt bis(dicarbollide) behaving like a classical surfactant. Despite their pristine structure resembling Platonic solids, the nature of anionic boron cluster compounds is inherently amphiphilic-they are stealth amphiphiles.

Insights into Protein-Ligand Interactions: Mechanisms, Models, and Methods

Molecular recognition, which is the process of biological macromolecules interacting with each other or various small molecules with a high specificity and affinity to form a specific complex, constitutes the basis of all processes in living organisms. Proteins, an important class of biological macromolecules, realize their functions through binding to themselves or other molecules. A detailed understanding of the protein–ligand interactions is therefore central to understanding biology at the molecular level. Moreover, knowledge of the mechanisms responsible for the protein-ligand recognition and binding will also facilitate the discovery, design, and development of drugs. In the present review, first, the physicochemical mechanisms underlying protein–ligand binding, including the binding kinetics, thermodynamic concepts and relationships, and binding driving forces, are introduced and rationalized. Next, three currently existing protein-ligand binding models—the “lock-and-key”, “induced fit”, and “conformational selection”—are described and their underlying thermodynamic mechanisms are discussed. Finally, the methods available for investigating protein–ligand binding affinity, including experimental and theoretical/computational approaches, are introduced, and their advantages, disadvantages, and challenges are discussed.

Direct insight into the nonclassical hydrophobic effect in bile salt:β-cyclodextrin interaction: role of hydrophobicity in governing the prototropism of a biological photosensitizer

The interaction of norharmane with bile salts is reported along with the evidence for nonclassical hydrophobic effect in bile salt:β-cyclodextrin interaction.

Thermodynamics of binding of structurally similar ligands to histone deacetylase 8 sheds light on challenges in the rational design of potent and isozyme-selective inhibitors of the enzyme

Among the different histone deacetylase (HDAC) isozymes, HDAC8 is the most highly malleable enzyme, and it exhibits the potential to accommodate structurally diverse ligands (albeit with moderate binding affinities) in its active site pocket. To probe the molecular basis of this feature, we performed detailed thermodynamic studies of the binding of structurally similar ligands, which differed with respect to the “cap”, “linker”, and “metal-binding” regions of the suberoylanilide hydroxamic acid (SAHA) pharmacophore, to HDAC8. The experimental data revealed that although the enthalpic (ΔH°) and entropic (ΔS°) changes for the binding of individual SAHA analogues to HDAC8 were substantially different, their binding free energies (ΔG°) were markedly similar, conforming to a strong enthalpy–entropy compensation effect. This effect was further observed in the temperature-dependent thermodynamics of binding of all SAHA analogues to the enzyme. Notably, in contrast to other metalloenzymes, our isothermal titration calorimetry experiments (performed in different buffers of varying ionization enthalpies) suggest that depending on the ligand, its zinc-binding group may or may not be deprotonated upon the binding to HDAC8. Furthermore, the heat capacity changes (ΔC_p°) associated with the ligand binding to HDAC8 markedly differed from one SAHA analogue to the other, and such features could primarily be rationalized in light of the dynamic flexibility in the enzyme structure in conjunction with the reorganization of the active site resident water molecules. Arguments are presented that although the binding thermodynamic features described above would facilitate identification of weak to moderately tight-binding HDAC8 inhibitors (by a high-throughput and/or virtual screening of libraries of small molecules), they would pose major challenges for the structure-based rational design of highly potent and isozyme-selective inhibitors of human HDAC8.

The structure, stability and pheromone binding of the male mouse protein sex pheromone darcin

Mouse urine contains highly polymorphic major urinary proteins that have multiple functions in scent communication through their abilities to bind, transport and release hydrophobic volatile pheromones. The mouse genome encodes for about 20 of these proteins and are classified, based on amino acid sequence similarity and tissue expression patterns, as either central or peripheral major urinary proteins. Darcin is a male specific peripheral major urinary protein and is distinctive in its role in inherent female attraction. A comparison of the structure and biophysical properties of darcin with MUP11, which belongs to the central class, highlights similarity in the overall structure between the two proteins. The thermodynamic stability, however, differs between the two proteins, with darcin being much more stable. Furthermore, the affinity of a small pheromone mimetic is higher for darcin, although darcin is more discriminatory, being unable to bind bulkier ligands. These attributes are due to the hydrophobic ligand binding cavity of darcin being smaller, caused by the presence of larger amino acid side chains. Thus, the physical and chemical characteristics of the binding cavity, together with its extreme stability, are consistent with darcin being able to exert its function after release into the environment.

Comparative study of the molecular variation between ‘central’ and ‘peripheral’ MUPs and significance for behavioural signalling

MUPs (major urinary proteins) play an important role in chemical signalling in rodents and possibly other animals. In the house mouse (Mus musculus domesticus) MUPs in urine and other bodily fluids trigger a range of behavioural responses that are only partially understood. There are at least 21 Mup genes in the C57BL/6 mouse genome, all located on chromosome 4, encoding sequences of high similarity. Further analysis separates the MUPs into two groups, the ‘central’ near-identical MUPs with over 97% sequence identity and the ‘peripheral’ MUPs with a greater degree of heterogeneity and approximately 20–30% non-conserved amino acids. This review focuses on differences between the two MUP sub-groups and categorizes these changes in terms of molecular structure and pheromone binding. As small differences in amino acid sequence can result in marked changes in behavioural response to the signal, we explore the potential of single amino acid changes to affect chemical signalling and protein stabilization. Using analysis of existing molecular structures available in the PDB we compare the chemical and physical properties of the ligand cavities between the MUPs. Furthermore, we identify differences on the solvent exposed surfaces of the proteins, which are characteristic of protein–protein interaction sites. Correlations can be seen between molecular heterogeneity and the specialized roles attributed to some MUPs.

Correlating structure and energetics in protein-ligand interactions: paradigms and paradoxes

Predicting protein-binding affinities of small molecules, even closely related ones, is a formidable challenge in biomolecular recognition and medicinal chemistry. A thermodynamic approach to optimizing affinity in protein-ligand interactions requires knowledge and understanding of how altering the structure of a small molecule will be manifested in protein-binding enthalpy and entropy changes; however, there is a relative paucity of such detailed information. In this review, we examine two strategies commonly used to increase ligand potency. The first of these involves introducing a cyclic constraint to preorganize a small molecule in its biologically active conformation, and the second entails adding nonpolar groups to a molecule to increase the amount of hydrophobic surface that is buried upon binding. Both of these approaches are motivated by paradigms suggesting that protein-binding entropy changes should become more favorable, but paradoxes can emerge that defy conventional wisdom.

An enthalpic basis of additivity in biphenyl hydroxamic acid ligands for stromelysin-1

Fragment based drug discovery remains a successful tool for pharmaceutical lead discovery. Although based upon the principle of thermodynamic additivity, the underlying thermodynamic basis is poorly understood. A thermodynamic additivity analysis was performed using stromelysin-1 and a series of biphenyl hydroxamate ligands identified through fragment additivity. Our studies suggest that, in this instance, additivity arises from enthalpic effects, while interaction entropies are unfavorable; this thermodynamic behavior is masked by proton transfer. Evaluation of the changes in constant pressure heat capacities during binding suggest that solvent exclusion from the binding site does not account for the dramatic affinity enhancements observed.

Fluoroalkyl and alkyl chains have similar hydrophobicities in binding to the "hydrophobic wall" of carbonic anhydrase

The hydrophobic effect, the free-energetically favorable association of nonpolar solutes in water, makes a dominant contribution to binding of many systems of ligands and proteins. The objective of this study was to examine the hydrophobic effect in biomolecular recognition using two chemically different but structurally similar hydrophobic groups, aliphatic hydrocarbons and aliphatic fluorocarbons, and to determine whether the hydrophobicity of the two groups could be distinguished by thermodynamic and biostructural analysis. This paper uses isothermal titration calorimetry (ITC) to examine the thermodynamics of binding of benzenesulfonamides substituted in the para position with alkyl and fluoroalkyl chains (H(2)NSO(2)C(6)H(4)-CONHCH(2)(CX(2))(n)CX(3), n = 0-4, X = H, F) to human carbonic anhydrase II (HCA II). Both alkyl and fluoroalkyl substituents contribute favorably to the enthalpy and the entropy of binding; these contributions increase as the length of chain of the hydrophobic substituent increases. Crystallography of the protein-ligand complexes indicates that the benzenesulfonamide groups of all ligands examined bind with similar geometry, that the tail groups associate with the hydrophobic wall of HCA II (which is made up of the side chains of residues Phe131, Val135, Pro202, and Leu204), and that the structure of the protein is indistinguishable for all but one of the complexes (the longest member of the fluoroalkyl series). Analysis of the thermodynamics of binding as a function of structure is compatible with the hypothesis that hydrophobic binding of both alkyl and fluoroalkyl chains to hydrophobic surface of carbonic anhydrase is due primarily to the release of nonoptimally hydrogen-bonded water molecules that hydrate the binding cavity (including the hydrophobic wall) of HCA II and to the release of water molecules that surround the hydrophobic chain of the ligands. This study defines the balance of enthalpic and entropic contributions to the hydrophobic effect in this representative system of protein and ligand: hydrophobic interactions, here, seem to comprise approximately equal contributions from enthalpy (plausibly from strengthening networks of hydrogen bonds among molecules of water) and entropy (from release of water from configurationally restricted positions).

High resolution X-ray structures of mouse major urinary protein nasal isoform in complex with pheromones

In mice, the major urinary proteins (MUP) play a key role in pheromonal communication by binding and transporting semiochemicals. MUP-IV is the only isoform known to be expressed in the vomeronasal mucosa. In comparison with the MUP isoforms that are abundantly excreted in the urine, MUP-IV is highly specific for the male mouse pheromone 2-sec-butyl-4,5-dihydrothiazole (SBT). To examine the structural basis of this ligand preference, we determined the X-ray crystal structure of MUP-IV bound to three mouse pheromones: SBT, 2,5-dimethylpyrazine, and 2-heptanone. We also obtained the structure of MUP-IV with 2-ethylhexanol bound in the cavity. These four structures show that relative to the major excreted MUP isoforms, three amino acid substitutions within the binding calyx impact ligand coordination. The F103 for A along with F54 for L result in a smaller cavity, potentially creating a more closely packed environment for the ligand. The E118 for G substitution introduces a charged group into a hydrophobic environment. The sidechain of E118 is observed to hydrogen bond to polar groups on all four ligands with nearly the same geometry as seen for the water-mediated hydrogen bond network in the MUP-I and MUP-II crystal structures. These differences in cavity size and interactions between the protein and ligand are likely to contribute to the observed specificity of MUP-IV.

Long-timescale molecular-dynamics simulations of the major urinary protein provide atomistic interpretations of the unusual thermodynamics of ligand binding

The mouse major urinary protein (MUP) has proved to be an intriguing test bed for detailed studies on protein-ligand recognition. NMR, calorimetric, and modeling investigations have revealed that the thermodynamics of ligand binding involve a complex interplay between competing enthalpic and entropic terms. We performed six independent, 1.2 micros molecular-dynamics simulations on MUP--three replicates on the apo-protein, and three on the complex with the pheromone isobutylmethoxypyrazine. Our findings provide the most comprehensive picture to date of the structure and dynamics of MUP, and how they are modulated by ligand binding. The mechanical pathways by which amino acid side chains can transmit information regarding ligand binding to surface loops and either increase or decrease their flexibility (entropy-entropy compensation) are identified. Dewetting of the highly hydrophobic binding cavity is confirmed, and the results reveal an aspect of ligand binding that was not observed in earlier, shorter simulations: bound ligand retains extensive rotational freedom. Both of these features have significant implications for interpretations of the entropic component of binding. More generally, these simulations test the ability of current molecular simulation methods to produce a reliable and reproducible picture of protein dynamics on the microsecond timescale.

A survey of the year 2007 literature on applications of isothermal titration calorimetry

Elucidation of the energetic principles of binding affinity and specificity is a central task in many branches of current sciences: biology, medicine, pharmacology, chemistry, material sciences, etc. In biomedical research, integral approaches combining structural information with in-solution biophysical data have proved to be a powerful way toward understanding the physical basis of vital cellular phenomena. Isothermal titration calorimetry (ITC) is a valuable experimental tool facilitating quantification of the thermodynamic parameters that characterize recognition processes involving biomacromolecules. The method provides access to all relevant thermodynamic information by performing a few experiments. In particular, ITC experiments allow to by-pass tedious and (rarely precise) procedures aimed at determining the changes in enthalpy and entropy upon binding by van't Hoff analysis. Notwithstanding limitations, ITC has now the reputation of being the "gold standard" and ITC data are widely used to validate theoretical predictions of thermodynamic parameters, as well as to benchmark the results of novel binding assays. In this paper, we discuss several publications from 2007 reporting ITC results. The focus is on applications in biologically oriented fields. We do not intend a comprehensive coverage of all newly accumulated information. Rather, we emphasize work which has captured our attention with originality and far-reaching analysis, or else has provided ideas for expanding the potential of the method.