Enthalpy/entropy compensation effects from cavity desolvation underpin broad ligand binding selectivity for rat odorant binding protein 3

Using Implicit-Solvent Potentials to Extract Water Contributions to Enthalpy-Entropy Compensation in Biomolecular Associations

Biomolecular assembly typically exhibits enthalpy-entropy compensation (EEC) behavior whose molecular origin remains a long-standing puzzle. While water restructuring is believed to play an important role in EEC, its contribution to the entropy and enthalpy changes, and how these changes relate to EEC, remains poorly understood. Here, we show that water reorganization entropy/enthalpy can be obtained by exploiting the temperature dependence in effective, implicit-solvent potentials. We find that the different temperature dependencies in the hydrophobic interaction, rooted in water reorganization, result in substantial variations in the entropy/enthalpy change, which are responsible for EEC. For lower-critical-solution-temperature association, water reorganization entropy dominates the free-energy change at the expense of enthalpy; for upper-critical-solution-temperature association, water reorganization enthalpy drives the process at the cost of entropy. Other effects, such as electrostatic interaction and conformation change of the macromolecules, contribute much less to the variations in entropy/enthalpy.

Ligand Binding Properties of Odorant-Binding Protein OBP5 from Mus musculus

Odorant-binding proteins (OBPs) are abundant soluble proteins secreted in the nasal mucus of a variety of species that are believed to be involved in the transport of odorants toward olfactory receptors. In this study, we report the functional characterization of mouse OBP5 (mOBP5). mOBP5 was recombinantly expressed as a hexahistidine-tagged protein in bacteria and purified using metal affinity chromatography. The oligomeric state and secondary structure composition of mOBP5 were investigated using gel filtration and circular dichroism spectroscopy. Fluorescent experiments revealed that mOBP5 interacts with the fluorescent probe N-phenyl naphthylamine (NPN) with micromolar affinity. Competitive binding experiments with 40 odorants indicated that mOBP5 binds a restricted number of odorants with good affinity. Isothermal titration calorimetry (ITC) confirmed that mOBP5 binds these compounds with association constants in the low micromolar range. Finally, protein homology modeling and molecular docking analysis indicated the amino acid residues of mOBP5 that determine its binding properties.

Odorant-binding proteins of mammals

Odorant-binding proteins (OBPs) of vertebrates belong to the lipocalin superfamily and perform a dual function: solubilizing and ferrying volatile pheromones to the olfactory receptors, and complexing the same molecules in specialized glands and assisting their release into the environment. Within vertebrates, to date they have been reported only in mammals, apart from two studies on amphibians. Based on the small number of OBPs expressed in each species, on their sites of production outside the olfactory area and their presence in biological fluids known to be pheromone carriers, such as urine, saliva and sexual secretions, we conclude that OBPs of mammals are specifically dedicated to pheromonal communication. This assumption is further supported by the observation that some OBPs present in biological secretions are endowed with their own pheromonal activity, adding renewed interest to these proteins. Another novel piece of evidence is the recent discovery that glycosylation and phosphorylation can modulate the binding activity of these proteins, improving their affinity to pheromones and narrowing their specificity. A comparison with insects and other arthropods shows a completely different scenario. While mammalian OBPs are specifically tuned to pheromones, those of insects, which are completely different in sequence and structure, include carriers for general odorants in addition to those dedicated to pheromones. Additionally, whereas mammals adopted a single family of carrier proteins for chemical communication, insects and other arthropods are endowed with several families of semiochemical-binding proteins. Here, we review the literature on the structural and functional properties of vertebrate OBPs, summarize the most interesting new findings and suggest possible exciting future developments.

Bacterial expression and purification of vertebrate odorant-binding proteins

Vertebrate odorant-binding proteins (OBPs) are small soluble proteins abundantly secreted in the olfactory mucus of many animal species, including humans. Vertebrate OBPs reversibly bind odorant molecules with micromolar range affinities. Although their physiological role is not clearly understood, OBPs are proposed to carry airborne odorants toward membrane olfactory receptors through the nasal mucus. Measurements of odorant-OBP interactions and structural studies require a large amount of pure OBPs devoid of ligands. The bacterial expression system is the first choice for expressing vertebrate OBPs used in our laboratory and others. This system generally produces OBPs in large amounts without major problems. In this chapter, we describe the milligram-scale production of recombinant pig OBP1 (pOBP1) in E. coli. The different steps of expression and purification are presented and discussed. Protocols for secondary structures investigation by circular dichroism and binding properties of the recombinant protein are also provided. More generally, these approaches can be used to produce and characterize any vertebrate OBPs for use in functional and structural studies.

Dose-related effects of inhaled essential oils on behavioural measures of anxiety and depression and biomarkers of oxidative stress

ETHNOPHARMACOLOGICAL RELEVANCE

Essential oils (EOs) are extracts of organic, volatile metabolites of plants that are typically oily liquids at ambient temperatures. Inhalation of EOs can regulate brain health and functions associated with mood and neurodegeneration, reflecting their bioavailability to brain. The aim was to identify physicochemical properties that influenced EO volatility and pathways of brain uptake by inhalation.

MATERIALS AND METHODS

Dose-dependency of effects, determined as: total EO intake (μg/g bodyweight-BW), and rate of EO intake (μg/hr/g-BW), was determined by meta-analysis of data from animal studies (10 studies, 12 EOs), measuring effects on anxiety, depression and selected biomarkers of oxidative stress and inflammation (OSI).

RESULTS

Results demonstrated benefits on animal behavior at EO intakes of 1-100 μg/g BW and 1-10 μg/hr/g BW (Elevated Plus Maze and Forced Swimming tests) and <100 μg/g BW and 10-100 g/hr/g BW (Marble Burying). EOs regulated OSI biomarkers at intakes of 10-100 μg/g BW and 1-10 μg/h/g BW, and a dose-dependent elevation of dopamine at >1000 μg/g BW and 100-1000 μg/hr/g BW.

CONCLUSION

The results support that EO 'aromatherapy' can promote dose-dependent regulation of anxiety, depression and OSI and that efficacy requires optimization of dose.

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.

A Hilly path through the thermodynamics and statistical mechanics of protein solutions

The opus of Don Winzor in the fields of physical and analytical biochemistry is a major component of that certain antipodean approach to this broad area of research that blossomed in the second half of the twentieth century. The need to formulate problems in terms of thermodynamic nonideality posed the challenge of describing a clear route from molecular interactions to the parameters that biochemists routinely measure. Mapping out this route required delving into the statistical mechanics of solutions of macromolecules, and at every turn mathematically complex, rigorous, general results that had previously been derived previously, often by Terrell Hill, came to the fore. Central to this work were the definition of the "thermodynamic activity", the pivotal position of the polynomial expansion of the osmotic pressure in terms of molar concentration and the relationship of virial coefficients to details of the forces between limited-size groups of interacting molecules. All of this was richly exploited in the task of taking account of excluded volume and electrostatic interactions, especially in the use of sedimentation equilibrium to determine values of constants for molecular association reactions. Such an approach has proved relevant to the study of molecular interactions generally, even those between the main macromolecular solute and components of the solvent, by using techniques such as exclusion and affinity chromatography as well as light scattering.

Impact of Surface Water Layers on Protein--Ligand Binding: How Well Are Experimental Data Reproduced by Molecular Dynamics Simulations in a Thermolysin Test Case?

Drug binding involves changes of the local water structure around proteins including water rearrangements across surface-solvation layers around protein and ligand portions exposed to the newly formed complex surface. For a series of thermolysin-binding phosphonamidates, we discovered that variations of the partly exposed P2'-substituents modulate binding affinity up to 10 kJ mol(-1) with even larger enthalpy/entropy partitioning of the binding signature. The observed profiles cannot be completely explained by desolvation effects. Instead, the quality and completeness of the surface water network wrapping around the formed complexes provide an explanation for the observed structure-activity relationship. We used molecular dynamics to compute surface water networks and predict solvation sites around the complexes. A fairly good correspondence with experimental difference electron densities in high-resolution crystal structures is achieved; in detail some problems with the potentials were discovered. Charge-assisted contacts to waters appeared as exaggerated by AMBER, and stabilizing contributions of water-to-methyl contacts were underestimated.

Unveiling prolyl oligopeptidase ligand migration by comprehensive computational techniques

Prolyl oligopeptidase (POP) is a large 80 kDa protease, which cleaves oligopeptides at the C-terminal side of proline residues and constitutes an important pharmaceutical target. Despite the existence of several crystallographic structures, there is an open debate about migration (entrance and exit) pathways for ligands, and their coupling with protein dynamics. Recent studies have shown the capabilities of molecular dynamics and classical force fields in describing spontaneous binding events and nonbiased ligand migration pathways. Due to POP's size and to the buried nature of its active site, an exhaustive sampling by means of conventional long enough molecular dynamics trajectories is still a nearly impossible task. Such a level of sampling, however, is possible with the breakthrough protein energy landscape exploration technique. Here, we present an exhaustive sampling of POP with a known inhibitor, Z-pro-prolinal. In >3000 trajectories Z-pro-prolinal explores all the accessible surface area, showing multiple entrance events into the large internal cavity through the pore in the β-propeller domain. Moreover, we modeled a natural substrate binding and product release by predicting the entrance of an undecapeptide substrate, followed by manual active site cleavage and nonbiased exit of one of the products (a dipeptide). The product exit shows preference from a flexible 18-amino acid residues loop, pointing to an overall mechanism where entrance and exit occur in different sites.

The tyrosine gate of the bacterial lectin FimH: a conformational analysis by NMR spectroscopy and X-ray crystallography

Urinary tract infections caused by uropathogenic E. coli are among the most prevalent infectious diseases. The mannose-specific lectin FimH mediates the adhesion of the bacteria to the urothelium, thus enabling host cell invasion and recurrent infections. An attractive alternative to antibiotic treatment is the development of FimH antagonists that mimic the physiological ligand. A large variety of candidate drugs have been developed and characterized by means of in vitro studies and animal models. Here we present the X-ray co-crystal structures of FimH with members of four antagonist classes. In three of these cases no structural data had previously been available. We used NMR spectroscopy to characterize FimH-antagonist interactions further by chemical shift perturbation. The analysis allowed a clear determination of the conformation of the tyrosine gate motif that is crucial for the interaction with aglycone moieties and was not obvious from X-ray structural data alone. Finally, ITC experiments provided insight into the thermodynamics of antagonist binding. In conjunction with the structural information from X-ray and NMR experiments the results provide a mechanism for the often-observed enthalpy-entropy compensation of FimH antagonists that plays a role in fine-tuning of the interaction.

Crystal structure of the human odorant binding protein, OBPIIa

Human odorant-binding protein, OBPIIa , is expressed by nasal epithelia to facilitate transport of hydrophobic odorant molecules across the aqueous mucus. Here, we report its crystallographic analysis at 2.6 Å resolution. OBPIIa is a monomeric protein that exhibits the classical lipocalin fold with a conserved eight-stranded β-barrel harboring a remarkably large hydrophobic pocket. Basic residues within the four loops that shape the entrance to this ligand-binding site evoke a positive electrostatic potential. Human OBPIIa shows distinct features compared with other mammalian OBPs, including a potentially reactive Cys side chain within its pocket similar to human tear lipocalin.

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.