Odorant binding and conformational dynamics in the odorant-binding protein

Unravelling the genomic landscape reveals the presence of six novel odorant-binding proteins in whitefly Bemisia tabaci Asia II-1

Genome wide analysis identified 14 OBPs in B. tabaci Asia II-1, of which six are new to science. Phylogenetic analysis traced their diversity and evolutionary lineage among Hemipteran insects. Comparative analysis reclassified the OBP gene families among B. tabaci cryptic species: Asia I, II-1, MEAM1, and MED. The 14 OBPs were clustered on four chromosomes of B. tabaci. RT-qPCR showed high expression of OBP3 and 8 across all body tissues and OBP10 in the abdomen. Molecular docking showed that OBP 3 and 10 had high affinity bonding with different candidate ligands, with binding energies ranging from -5.0 to -7.7 kcal/mol. Competitive fluorescence binding assays revealed that β-caryophyllene and limonene had high binding affinities for OBP3 and 10, with their IC50 values ranging from 9.16 to 14 μmol·L-1 and KD values around 7 to 9 μmol·L-1. Behavioural assays revealed that β-caryophyllene and carvacrol were attractants, β-ocimene and limonene were repellents, and γ-terpinene and β-ocimene were oviposition deterrents to B. tabaci. Functional validation by RNAi demonstrated that OBP3 and OBP10 modulated host recognition of B. tabaci. This study expands our understanding of the genomic landscape of OBPs in B. tabaci, offering scope for developing novel pest control strategies.

Pheromones, binding proteins, and olfactory systems in the pig (Sus scrofa): An updated review

Pigs utilize multimodal communication for reproductive and other behaviors, and chemical communication is one of the key components. The success of reproduction relies on chemical communication favored by the steroid pheromones from boar saliva. These steroids were proven to be involved in advancing puberty in gilts (the boar effect) and in promoting estrus behaviors in gilts/sows, thereby helping to detect estrus and facilitating the timing of artificial insemination. The steroid pheromones bound with carrier proteins are evidenced in the mandibular (submandibular) salivary secretions of the boar. These salivary steroids bind with carrier proteins in the nasal mucus and vomeronasal organ (VNO) of the sows, eventually triggering a cascade of activities at the olfactory and endocrine levels. Besides steroid pheromones, pig appeasing pheromones (from mammary skin secretions of sows) have also been demonstrated to bind with carrier proteins in the nasal mucus and VNO of the piglets. Thus far, four different proteins have been identified and confirmed in the nasal mucus and VNO of pigs, including odorant binding proteins (OBPs), salivary lipocalin (SAL), pheromaxein, and Von Ebner's Gland Protein (VEGP). The critical roles of the chemosensory systems, main olfactory systems and VNO, have been comprehensively reported for pigs. This review summarizes the current knowledge on pheromones, their receptor proteins, and the olfactory systems of porcine species.

Antennal Enriched Odorant Binding Proteins Are Required for Odor Communication in Glossina f. fuscipes

Olfaction is orchestrated at different stages and involves various proteins at each step. For example, odorant-binding proteins (OBPs) are soluble proteins found in sensillum lymph that might encounter odorants before reaching the odorant receptors. In tsetse flies, the function of OBPs in olfaction is less understood. Here, we investigated the role of OBPs in Glossina fuscipes fuscipes olfaction, the main vector of sleeping sickness, using multidisciplinary approaches. Our tissue expression study demonstrated that GffLush was conserved in legs and antenna in both sexes, whereas GffObp44 and GffObp69 were expressed in the legs but absent in the antenna. GffObp99 was absent in the female antenna but expressed in the male antenna. Short odorant exposure induced a fast alteration in the transcription of OBP genes. Furthermore, we successfully silenced a specific OBP expressed in the antenna via dsRNAi feeding to decipher its function. We found that silencing OBPs that interact with 1-octen-3-ol significantly abolished flies' attraction to 1-octen-3-ol, a known attractant for tsetse fly. However, OBPs that demonstrated a weak interaction with 1-octen-3-ol did not affect the behavioral response, even though it was successfully silenced. Thus, OBPs' selective interaction with ligands, their expression in the antenna and their significant impact on behavior when silenced demonstrated their direct involvement in olfaction.

Biotechnological applications of mammalian odorant-binding proteins

The olfactory system of mammals allows the detection and discrimination of thousands of odors from the environment. In mammals, odorant-binding proteins (OBPs) are considered responsible to carry odorant molecules across the aqueous nasal mucus to the olfactory receptors (ORs). The three-dimensional structure of these proteins presents eight antiparallel β-sheets and a short α-helical segment close to the C terminus, typical of the lipocalins family. The great ability of OBPs to bind differentiated ligand molecules has driven the research to understand the mechanisms underlying the OBP function in nature and the development of advanced biotechnological applications. This review describes the role of mammalian OBPs in the olfactory perception, highlighting the influence of several key parameters (amino acids, temperature, ionic strength, and pH) in the formation of the OBP/ligand complex. The information from the literature regarding OBP structure, affinity, the strength of binding, and stability inspiring the development of several applications herein detailed.

Plasmonic biosensors relying on biomolecular conformational changes: Case of odorant binding proteins

Plasmonic nanostructures serve in a range of analytical techniques that were developed for the analysis of chemical and biological species. Among others, they have been pursued for the investigation of odorant binding proteins (OBP) and their interaction with odorant molecules. These compounds are low molecular weight agents, which makes their direct detection with conventional surface plasmon resonance (SPR) challenging. Therefore, other plasmonic sensor modalities need to be implemented for the detection and interaction analysis of OBPs. This chapter provides a guide for carrying out such experiments based on two techniques that take advantage of conformation changes of OBPs occurring upon specific interaction with their affinity partners. First, there is discussed SPR monitoring of conformation changes of biomolecules that are not accompanied by a strong increase in the surface mass density but rather with its re-distribution perpendicular to the surface. Second, the implementation of surface plasmon-enhanced fluorescence energy transfer is presented for the sensitive monitoring of conformational changes of biomolecules tagged with a fluorophore at its defined part. Examples from our and other laboratories illustrate the performance of these concepts and their applicability for the detection of low molecular weight odorant molecules by the use of OBPs attached to the sensor surface is discussed.

Bio-Inspired Strategies for Improving the Selectivity and Sensitivity of Artificial Noses: A Review

Artificial noses are broad-spectrum multisensors dedicated to the detection of volatile organic compounds (VOCs). Despite great recent progress, they still suffer from a lack of sensitivity and selectivity. We will review, in a systemic way, the biomimetic strategies for improving these performance criteria, including the design of sensing materials, their immobilization on the sensing surface, the sampling of VOCs, the choice of a transduction method, and the data processing. This reflection could help address new applications in domains where high-performance artificial noses are required such as public security and safety, environment, industry, or healthcare.

Effects of point mutations in the binding pocket of the mouse major urinary protein MUP20 on ligand affinity and specificity

The mouse Major Urinary Proteins (MUPs) contain a conserved β-barrel structure with a characteristic central hydrophobic pocket that binds a variety of volatile compounds. After release of urine, these molecules are slowly emitted in the environment where they play an important role in chemical communication. MUPs are highly polymorphic and conformationally stable. They may be of interest in the construction of biosensor arrays capable of detection of a broad range of analytes. In this work, 14 critical amino acids in the binding pocket involved in ligand interactions were identified in MUP20 using in silico techniques and 7 MUP20 mutants were synthesised and characterised to produce a set of proteins with diverse ligand binding profiles to structurally different ligands. A single amino acid substitution in the binding pocket can dramatically change the MUPs binding affinity and ligand specificity. These results have great potential for the design of new biosensor and gas-sensor recognition elements.

1-Aminoanthracene Transduction into Liposomes Driven by Odorant-Binding Protein Proximity

In this work, the anchorage of pig odorant binding protein (OBP-I) into liposomal membrane was promoted by the fusion of OBP-I with the anchor SP-DS3 peptide and with the (GQ)₂₀ spacer. The presence of the (GQ)₂₀ spacer in the construct confers flexibility to the protein and increases the distance between the OBP binding site and the liposomal surface. The engineered proteins, OBP::SP-DS3 and OBP::(GQ)₂₀::SP-DS3, were produced in Escherichia coli BL21(DE3) and characterized by circular dichroism spectroscopy and MALDI-TOF. The functionalization of liposomes with the OBP proteins was performed through ethanol injection, and similar liposomal anchorage (∼92-97%) was found for both OBP constructs. The effect of OBPs' proximity to the liposomes membrane on 1-aminoanthracene (1-AMA, model ligand) transduction was evaluated by measuring the amount of 1-AMA transduced into liposomes by fluorescence spectroscopy. While protein flexibility, given by the presence of the (GQ)₂₀ spacer, seems to influence the binding efficiency, ∼45% for OBP::(GQ)₂₀::SP-DS3 and ∼29% for OBP::SP-DS3, the distance between the proteins' binding site and the liposomal membrane determines their ability to transduce the 1-AMA into the liposomes (∼23% for OBP::SP-DS3 and ∼19% for OBP::(GQ)₂₀::SP-DS3). The anchorage capacity and proximity effect were confirmed by an experimental control where the wild-type (wt) OBP was added to the liposomes, resulting in low 1-AMA transduction (∼3.5%) and low binding to OBPwt (∼9%). These findings evidence the effect of anchorage, carrier protein's flexibility, and proximity as key features for the entrapment of molecules into the liposomal membrane. The developed OBP-based devices are thus promising anchorage systems for the capture and storage of odors with potential applications in textile and cosmetic industries.

The Pig Olfactory Brain: A Primer

Despite the fact that pigs are reputed to have excellent olfactory abilities, few studies have examined regions of the pig brain involved in the sense of smell. The present study provides an overview of the olfactory bulb, anterior olfactory nucleus, and piriform cortex of adult pigs using several approaches. Nissl, myelin, and Golgi stains were used to produce a general overview of the organization of the regions and confocal microscopy was employed to examine 1) projection neurons, 2) GABAergic local circuit neurons that express somatostatin, parvalbumin, vasoactive intestinal polypeptide, or calretinin, 3) neuromodulatory fibers (cholinergic and serotonergic), and 4) glia (astrocytes and microglia). The findings revealed that pig olfactory structures are quite large, highly organized and follow the general patterns observed in mammals.

A sand fly salivary protein vaccine shows efficacy against vector-transmitted cutaneous leishmaniasis in nonhuman primates

Currently, there are no commercially available human vaccines against leishmaniasis. In rodents, cellular immunity to salivary proteins of sand fly vectors is associated to protection against leishmaniasis, making them worthy targets for further exploration as vaccines. We demonstrate that nonhuman primates (NHP) exposed to Phlebotomus duboscqi uninfected sand fly bites or immunized with salivary protein PdSP15 are protected against cutaneous leishmaniasis initiated by infected bites. Uninfected sand fly-exposed and 7 of 10 PdSP15-immunized rhesus macaques displayed a significant reduction in disease and parasite burden compared to controls. Protection correlated to the early appearance of Leishmania-specific CD4(+)IFN-γ(+) lymphocytes, suggesting that immunity to saliva or PdSP15 augments the host immune response to the parasites while maintaining minimal pathology. Notably, the 30% unprotected PdSP15-immunized NHP developed neither immunity to PdSP15 nor an accelerated Leishmania-specific immunity. Sera and peripheral blood mononuclear cells from individuals naturally exposed to P. duboscqi bites recognized PdSP15, demonstrating its immunogenicity in humans. PdSP15 sequence and structure show no homology to mammalian proteins, further demonstrating its potential as a component of a vaccine for human leishmaniasis.

Operating mechanism and molecular dynamics of pheromone-binding protein ASP1 as influenced by pH

Odorant binding protein (OBP) is a vital component of the olfactory sensation system. It performs the specific role of ferrying odorant molecules to odorant receptors. OBP helps insects and types of animal to sense and transport stimuli molecules. However, the molecular details about how OBPs bind or release its odorant ligands are unclear. For some OBPs, the systems' pH level is reported to impact on the ligands' binding or unbinding capability. In this work we investigated the operating mechanism and molecular dynamics in bee antennal pheromone-binding protein ASP1 under varying pH conditions. We found that conformational flexibility is the key factor for regulating the interaction of ASP1 and its ligands, and the odorant binds to ASP1 at low pH conditions. Dynamics, once triggered by pH changes, play the key roles in coupling the global conformational changes with the odorant release. In ASP1, the C-terminus, the N-terminus, helix α2 and the region ranging from helices α4 to α5 form a cavity with a novel 'entrance' of binding. These are the major regions that respond to pH change and regulate the ligand release. Clearly there are processes of dynamics and hydrogen bond network propagation in ASP1 in response to pH stimuli. These findings lead to an understanding of the mechanism and dynamics of odorant-OBP interaction in OBP, and will benefit chemsensory-related biotech and agriculture research and development.

Lipocalin-type prostaglandin D synthase scavenges biliverdin in the cerebrospinal fluid of patients with aneurysmal subarachnoid hemorrhage

Lipocalin-type prostaglandin (PG) D synthase (L-PGDS) is the second major protein in human cerebrospinal fluid (CSF) and belongs to the lipocalin superfamily composed of various secretory lipophilic ligand transporter proteins. However, the endogenous ligand of L-PGDS has not yet been elucidated. In this study, we purified L-PGDS from the CSF of aneurysmal subarachnoid hemorrhage (SAH) patients. Lipocalin-type PG D synthase showed absorbance spectra with major peaks at 280 and 392 nm and a minor peak at around 660 nm. The absorbance at 392 nm of L-PGDS increased from 1 to 9 days and almost disappeared at 2 months after SAH, whereas the L-PGDS activity decreased from 1 to 7 days and recovered to normal at 2 months after SAH. These results indicate that some chromophore had accumulated in the CSF after SAH and bound to L-PGDS, thus inactivating it. Matrix assisted laser desorption ionization time-of-flight mass spectrometry of L-PGDS after digestion of it with endoproteinase Lys-C revealed that L-PGDS had covalently bound biliverdin, a by-product of heme breakdown. These results suggest that L-PGDS acted as a scavenger of biliverdin, which is a molecule not found in normal CSF. This is the first report of identification of a pathophysiologically important endogenous ligand for this lipocalin superfamily protein in humans.

A computational microscope focused on the sense of smell

In this article, we review studies of the protagonists of the perception of smell focusing on Odorant-Binding Proteins and Olfactory Receptors. We notably put forward studies performed by means of molecular modeling, generally combined with experimental data. Those works clearly emphasize that computational approaches are now a force to reckon with. In the future, they will certainly be more and more used, notably in the framework of a computational microscope meant to observe how the laws of physics govern the biomolecular systems originating our sense of smell.

Protein-Ligand Binding from Distancefield Distances and Hamiltonian Replica Exchange Simulations

The calculation of protein-ligand binding free energies is an important goal in the field of computational chemistry. Applying path-sampling methods for this purpose involves calculating the associated potential of mean force (PMF) and gives insight into the binding free energy along the binding process. Without a priori knowledge about the binding path, sampling reversible binding can be difficult to achieve. To alleviate this problem, we introduce the distancefield (DF) as a reaction coordinate for such calculations. DF is a grid-based method in which the shortest distance between the binding site and a ligand is determined avoiding routes that pass through the protein. Combining this reaction coordinate with Hamiltonian replica exchange molecular dynamics (HREMD) allows for the reversible binding of the ligand to the protein. A comparison is made between umbrella sampling using regular distance restraints and HREMD with DF restraints to study aspirin binding to the protein phospholipase A2. Although the free energies of binding are similar for both methods, the increased sampling with HREMD has a significant influence on the shape of the PMF. A remarkable agreement between the calculated binding free energies from the PMF and the experimental estimate is obtained.

Functional dissection of Odorant binding protein genes in Drosophila melanogaster

Most organisms rely on olfaction for survival and reproduction. The olfactory system of Drosophila melanogaster is one of the best characterized chemosensory systems and serves as a prototype for understanding insect olfaction. Olfaction in Drosophila is mediated by multigene families of odorant receptors and odorant binding proteins (OBPs). Although molecular response profiles of odorant receptors have been well documented, the contributions of OBPs to olfactory behavior remain largely unknown. Here, we used RNAi-mediated suppression of Obp gene expression and measurements of behavioral responses to 16 ecologically relevant odorants to systematically dissect the functions of 17 OBPs. We quantified the effectiveness of RNAi-mediated suppression by quantitative real-time polymerase chain reaction and used a proteomic liquid chromatography and tandem mass spectrometry procedure to show target-specific suppression of OBPs expressed in the antennae. Flies in which expression of a specific OBP is suppressed often show altered behavioral responses to more than one, but not all, odorants, in a sex-dependent manner. Similarly, responses to a specific odorant are frequently affected by suppression of expression of multiple, but not all, OBPs. These results show that OBPs are essential for mediating olfactory behavioral responses and suggest that OBP-dependent odorant recognition is combinatorial.

Rapid odorant release in mammalian odour binding proteins facilitates their temporal coupling to odorant signals

We have measured the effect of rat odorant-binding protein 1 on the rates of ligand uptake and liquid-to-air transfer rates with a set of defined odorous compounds. Comparison of observed rate constants (k(obs)) with data simulated over a wide range of different kinetic and thermodynamic regimes shows that the data do not agree with the previously held view of a slow off-rate regime (k(off) <0.0004 s(-1)). We propose that a rapid k(off) would be a necessary requirement for such a system, since slow odorant-release rates would result in significant decorrelation between the olfactory world and odour perception.

Structural analysis of lipocalin-type prostaglandin D synthase complexed with biliverdin by small-angle X-ray scattering and multi-dimensional NMR

Lipocalin-type prostaglandin D synthase (L-PGDS) acts as both a PGD(2) synthase and an extracellular transporter for small lipophilic molecules. From a series of biochemical studies, it has been found that L-PGDS has an ability to bind a variety of lipophilic ligands such as biliverdin, bilirubin and retinoids in vitro. Therefore, we considered that it is necessary to clarify the molecular structure of L-PGDS upon binding ligand in order to understand the physiological relevance of L-PGDS as a transporter protein. We investigated a molecular structure of L-PGDS/biliverdin complex by small-angle X-ray scattering (SAXS) and multi-dimensional NMR measurements, and characterized the binding mechanism in detail. SAXS measurements revealed that L-PGDS has a globular shape and becomes compact by 1.3A in radius of gyration on binding biliverdin. NMR experiments revealed that L-PGDS possessed an eight-stranded antiparallel beta-barrel forming a central cavity. Upon the titration with biliverdin, some cross-peaks for residues surrounding the cavity and EF-loop and H2-helix above the beta-barrel shifted, and the intensity of other cross-peaks decreased with signal broadenings in (1)H-(15)N heteronuclear single quantum coherence spectra. These results demonstrate that L-PGDS holds biliverdin within the beta-barrel, and the conformation of the loop regions above the beta-barrel changes upon binding biliverdin. Through such a conformational change, the whole molecule of L-PGDS becomes compact.

Binding free energy prediction in strongly hydrophobic biomolecular systems

We present a comparison of various computational approaches aiming at predicting the binding free energy in ligand-protein systems where the ligand is located within a highly hydrophobic cavity. The relative binding free energy between similar ligands is obtained by means of the thermodynamic integration (TI) method and compared to experimental data obtained through isothermal titration calorimetry measurements. The absolute free energy of binding prediction was obtained on a similar system (a pyrazine derivative bound to a lipocalin) by TI, potential of mean force (PMF) and also by means of the MMPBSA protocols. Although the TI protocol performs poorly either with an explicit or an implicit solvation scheme, the PMF calculation using an implicit solvation scheme leads to encouraging results, with a prediction of the binding affinity being 2 kcal mol(-1) lower than the experimental value. The use of an implicit solvation scheme appears to be well suited for the study of such hydrophobic systems, due to the lack of water molecules within the binding site.

Standard Free Energy of Binding from a One-Dimensional Potential of Mean Force

A practical approach that enables one to calculate the standard free energy of binding from a one-dimensional potential of mean force (PMF) is proposed. Umbrella sampling and the weighted histogram analysis method are used to generate a PMF along the reaction coordinate of binding. At each point, a restraint is applied orthogonal to the reaction coordinate to make possible the determination of the volume sampled by the ligand. The free energy of binding from an arbitrary unbound volume to the restrained bound form is calculated from the ratio of the PMF integrated over the bound region to that of the unbound. Adding the free energy changes from the standard-state volume to the unbound volume and from the restrained to the unrestrained bound state gives the standard free energy of binding. Exploration of the best choice of binding paths is also made. This approach is first demonstrated on a model binding system and then tested on the benzamidine-trypsin system for which reasonable agreement with experiment is found. A comparison is made with other methods to obtain the standard free energy of binding from the PMF.

Mechanistic events underlying odorant binding protein chemoreception

Odorant binding proteins (OBP's) are small hydrophilic proteins, belonging to the lipocalin family dedicated to bind and transport small hydrophobic ligands. Despite many works, the mechanism of ligand binding, together with the functional role of these proteins remains a topic of debate and little is known at the atomic level. The present work reports a computational study of odorants capture and release by an OBP, using both constrained and unconstrained simulations, giving a glimpse on the molecular mechanism of chemoreception. The residues at the origin of the regulation of the protein door opening are identified and a tyrosine amino-acid together with other nearby residues appear to play a crucial role in allowing this event to occur. The simulations reveal that this tyrosine and the protein's L5 loop are implicated in the ligand contact with the protein and act as an anchoring point for the ligand. The protein structural features required for the ligand entry are highly conserved among many transport proteins, suggesting that this mechanism could somewhat be extended to some members of the larger family of lipocalin.

Responses of the rat olfactory epithelium to retronasal air flow

Responses of the rat olfactory epithelium were assessed with the electroolfactogram while odorants were presented to the external nares with an artificial sniff or to the internal nares by positive pressure. A series of seven odorants that varied from very polar, hydrophilic odorants to very nonpolar, hydrophobic odorants were used. Although the polar odorants activated the dorsal olfactory epithelium when presented by the external nares (orthonasal presentation), they were not effective when forced through the nasal cavity from the internal nares (retronasal presentation). However, the nonpolar odorants were effective in both stimulus modes. These results were independent of stimulus concentration or of humidity of the carrier air. Similar results were obtained with multiunit recordings from olfactory bulb. These results help to explain why human investigations often report differences in the sensation or ability to discriminate odorants presented orthonasally versus retronasally. The results also strongly support the importance of odorant sorption in normal olfactory processes.