An asymmetric dimer of beta-lactoglobulin in a low humidity crystal form--structural changes that accompany partial dehydration and protein action

Integrated spectroscopic and computational analyses unravel the molecular interaction of pesticide azinphos-methyl with bovine beta-lactoglobulin

Organophosphorus are typically hazardous chemicals used in the pharmaceutical, agricultural, and other industries. They pose a serious risk to human life and can be fatal upon direct exposure. Hence, studying the interaction between such compounds with proteins is crucial for environmental, health, and food safety. In this study, we investigated the interaction mechanism between azinphos-methyl (AZM) and β-lactoglobulin (BLG) at pH 7.4 using a combination of biophysical techniques. Intrinsic fluorescence investigations revealed that BLG fluorescence was quenched in the presence of increasing AZM concentrations. The quenching mechanism was identified as static, as evidenced by a decrease in the fluorescence quenching constant (1.25 × 104, 1.18 × 104, and 0.86 × 104 M-1) with an increase in temperatures. Thermodynamic calculations (ΔH > 0; ΔS > 0) affirmed the formation of a complex between AZM and BLG through hydrophobic interactions. The BLG's secondary structure was found to be increased due to AZM interaction. Ultraviolet -visible spectroscopy data showed alterations in BLG conformation in the presence of AZM. Molecular docking highlighted the significant role of hydrophobic interactions involving residues such as Val43, Ile56, Ile71, Val92, Phe105, and Met107 in the binding between BLG and AZM. A docking energy of -6.9 kcal mol-1, and binding affinity of 1.15 × 105 M-1 suggest spontaneous interaction between AZM and BLG with moderate to high affinity. These findings underscore the potential health risks associated with the entry of AZM into the food chain, emphasizing the need for further consideration of its impact on human health.

Architecture of β-lactoglobulin coating modulates bioinspired alginate dialdehyde-gelatine/polydopamine scaffolds for subchondral bone regeneration

In this study, we developed polydopamine (PDA)-functionalized alginate dialdehyde-gelatine (ADA-GEL) scaffolds for subchondral bone regeneration. These polymeric scaffolds were then coated with β-Lactoglobulin (β-LG) at concentrations of 1 mg/ml and 2 mg/ml. Morphological analysis indicated a homogeneous coating of the β-LG layer on the surface of network-like scaffolds. The β-LG-coated scaffolds exhibited improved swelling capacity as a function of the β-LG concentration. Compared to ADA-GEL/PDA scaffolds, the β-LG-coated scaffolds demonstrated delayed degradation and enhanced biomineralization. Here, a lower concentration of β-LG showed long-lasting stability and superior biomimetic hydroxyapatite mineralization. According to the theoretical findings, the single-state, representing the low concentration of β-LG, exhibited a homogeneous distribution on the surface of the PDA, while the dimer-state (high concentration) displayed a high likelihood of uncontrolled interactions. β-LG-coated ADA-GEL/PDA scaffolds with a lower concentration of β-LG provided a biocompatible substrate that supported adhesion, proliferation, and alkaline phosphatase (ALP) secretion of sheep bone marrow mesenchymal stem cells, as well as increased expression of osteopontin (SPP1) and collagen type 1 (COL1A1) in human osteoblasts. These findings indicate the potential of protein-coated scaffolds for subchondral bone tissue regeneration. STATEMENT OF SIGNIFICANCE: This study addresses a crucial aspect of osteochondral defect repair, emphasizing the pivotal role of subchondral bone regeneration. The development of polydopamine-functionalized alginate dialdehyde-gelatine (ADA-GEL) scaffolds, coated with β-Lactoglobulin (β-LG), represents a novel approach to potentially enhance subchondral bone repair. β-LG, a milk protein rich in essential amino acids and bioactive peptides, is investigated for its potential to promote subchondral bone regeneration. This research explores computationally and experimentally the influence of protein concentration on the ordered or irregular deposition, unravelling the interplay between coating structure, scaffold properties, and in-vitro performance. This work contributes to advancing ordered protein coating strategies for subchondral bone regeneration, providing a biocompatible solution with potential implications for supporting subsequent cartilage repair.

Structural evolution of pea-derived albumins during pH and heat treatment studied with light and X-ray scattering

Pea albumins are found in the side stream during the isolation of pea proteins. They are soluble at acidic pH and have functional properties which differ from their globulin counterparts. In this study, we have investigated the aggregation and structural changes occurring to pea albumins under different environmental conditions, using a combination of size-exclusion chromatography coupled with multi-angle laser light scattering (SEC-MALS) and small-angle X-ray scattering (SAXS). Albumins were extracted from a dry fractionated pea protein concentrate by precipitating the globulin fraction at acidic pH. The albumins were then studied at different pH (3, 4, 4.5, 7, 7.5, and 8) values. The effect of heating at 90 °C for 1, 3, and 5 min on their structural changes was investigated using SAXS. In addition, size exclusion of the albumins showed 4 distinct populations, depending on pH and heating conditions, with two large aggregates peaks (∼250 kDa): a dimer peak (∼24 kDa) containing predominantly pea albumin 2 (PA2), and a monomer peak of a molar mass of about 12 kDa (PA1). X-ray scattering intensities as a function of q were modeled as polydisperse spheres, and their aggregation was followed as a function of heating time. Albumins was most stable at pH 3, showing no aggregation during heat treatment. While albumins at pH 7.5 and 8 showed aggregation after heating, solutions at pH 4, 4.5, and 7 already contained aggregates even before heating. This work provides new knowledge on the overall structural development of albumins under different environmental conditions, improving our ability to employ these as future ingredients in foods.

Animal-derived food allergen: A review on the available crystal structure and new insights into structural epitope

Immunoglobulin E (IgE)-mediated food allergy is a rapidly growing public health problem. The interaction between allergens and IgE is at the core of the allergic response. One of the best ways to understand this interaction is through structural characterization. This review focuses on animal-derived food allergens, overviews allergen structures determined by X-ray crystallography, presents an update on IgE conformational epitopes, and explores the structural features of these epitopes. The structural determinants of allergenicity and cross-reactivity are also discussed. Animal-derived food allergens are classified into limited protein families according to structural features, with the calcium-binding protein and actin-binding protein families dominating. Progress in epitope characterization has provided useful information on the structural properties of the IgE recognition region. The data reveals that epitopes are located in relatively protruding areas with negative surface electrostatic potential. Ligand binding and disulfide bonds are two intrinsic characteristics that influence protein structure and impact allergenicity. Shared structures, local motifs, and shared epitopes are factors that lead to cross-reactivity. The structural properties of epitope regions and structural determinants of allergenicity and cross-reactivity may provide directions for the prevention, diagnosis, and treatment of food allergies. Experimentally determined structure, especially that of antigen-antibody complexes, remains limited, and the identification of epitopes continues to be a bottleneck in the study of animal-derived food allergens. A combination of traditional immunological techniques and emerging bioinformatics technology will revolutionize how protein interactions are characterized.

Limited Lactosylation of Beta-Lactoglobulin from Cow's Milk Exerts Strong Influence on Antigenicity and Degranulation of Mast Cells

Background: beta-lactoglobulin (BLG) is one of the major cow’s milk proteins and the most abundant allergen in whey. Heating is a common technologic treatment applied during milk transformational processes. Maillardation of BLG in the presence of reducing sugars and elevated temperatures may influence its antigenicity and allergenicity. Primary objective: to analyze and identify lactosylation sites by capillary electrophoresis mass spectrometry (CE-MS). Secondary objective: to assess the effect of lactosylated BLG on antigenicity and degranulation of mast cells. Methods: BLG was lactosylated at pH 7, a water activity (aw) of 0.43, and a temperature of 65 °C using a molar ratio BLG:lactose of 1:1 by incubating for 0, 3, 8, 16 or 24 h. For the determination of the effect on antibody-binding capacity of lactosylated BLG, an ELISA was performed. For the assessment of degranulation of the cell-line RBL-hεIa-2B12 transfected with the human α-chain, Fcε receptor type 1 (FcεRI) was used. Results: BLG showed saturated lactosylation between 8 and 16 incubation hours in our experimental setup. Initial stage lactosylation sites L1 (N-terminus)—K47, K60, K75, K77, K91, K138 and K141—have been identified using CE-MS. Lactosylated BLG showed a significant reduction of both the IgG binding (p = 0.0001) as well as degranulation of anti-BLG IgE-sensitized RBL-hεIa-2B12 cells (p < 0.0001). Conclusions and clinical relevance: this study shows that lactosylation of BLG decreases both the antigenicity and degranulation of mast cells and can therefore be a promising approach for reducing allergenicity of cow’s milk allergens provided that the process is well-controlled.

β-Lactoglobulin and Glycodelin: Two Sides of the Same Coin?

The two lipocalins, β-lactoglobulin (βLg) and glycodelin (Gd), are possibly the most closely related members of the large and widely distributed lipocalin family, yet their functions appear to be substantially different. Indeed, the function of β-lactoglobulin, a major component of ruminant milk, is still unclear although neonatal nutrition is clearly important. On the other hand, glycodelin has several specific functions in reproduction conferred through distinct, tissue specific glycosylation of the polypeptide backbone. It is also associated with some cancer outcomes. The glycodelin gene, PAEP, reflecting one of its names, progestagen-associated endometrial protein, is expressed in many though not all primates, but the name has now also been adopted for the β-lactoglobulin gene (HGNC, www.genenames.org). After a general overview of the two proteins in the context of the lipocalin family, this review considers the properties of each in the light of their physiological functional significance, supplementing earlier reviews to include studies from the past decade. While the biological function of glycodelin is reasonably well defined, that of β-lactoglobulin remains elusive.

Binding parameters and molecular dynamics of β-lactoglobulin-vanillic acid complexation as a function of pH - Part A: Acidic pH

Protein-phenolic compound interactions are commonly investigated with inappropriate linear equations for the analysis of binding strength and stoichiometry. This work utilises more appropriate protocols for the investigation of molecular interactions between vanillic acid and β-lactoglobulin at pH 2.4, where the protein predominately exists as a monomer. Non-linear binding and Job plot analysis were conducted on fluorescence data to effectively determine the interaction's dissociation constant (K_D, 2.93 × 10^-5 M) and stoichiometry (1:1). Furthermore, spectroscopic techniques revealed statistically significant alterations to the conformational characteristics of β-lactoglobulin upon complexation. Molecular dynamics (MD) simulations support a 1:1 interaction stoichiometry and reveal that the stabilisation of vanillic acid was dynamic in nature but mainly supported by four π-alkyl interactions and one hydrogen bond, located within the β-barrel of the monomer. Water molecules, which are generally not accounted for in MD simulation analysis, were shown to be an important factor in the ligand stabilization via bridging interactions.

Synchronous RNA conformational changes trigger ordered phase transitions in crystals

Time-resolved studies of biomacromolecular crystals have been limited to systems involving only minute conformational changes within the same lattice. Ligand-induced changes greater than several angstroms, however, are likely to result in solid-solid phase transitions, which require a detailed understanding of the mechanistic interplay between conformational and lattice transitions. Here we report the synchronous behavior of the adenine riboswitch aptamer RNA in crystal during ligand-triggered isothermal phase transitions. Direct visualization using polarized video microscopy and atomic force microscopy shows that the RNA molecules undergo cooperative rearrangements that maintain lattice order, whose cell parameters change distinctly as a function of time. The bulk lattice order throughout the transition is further supported by time-resolved diffraction data from crystals using an X-ray free electron laser. The synchronous molecular rearrangements in crystal provide the physical basis for studying large conformational changes using time-resolved crystallography and micro/nanocrystals.

Time-resolved crystallography (TRX) is used for monitoring only small conformational changes of biomacromolecules within the same lattice. Here, the authors report the interplay between synchronous molecular rearrangements and lattice phase transitions in RNA crystals, providing the basis for the investigation of large conformational changes using TRX.

β-Lactoglobulin-gold nanoparticles interface and its interaction with some anticancer drugs - an approach for targeted drug delivery

The protein-nanoparticle interface plays a crucial role in drug binding and stability, in turn enhancing efficacy in targeted drug delivery. In the present study, whey protein β-lactoglobulin (BLG) is conjugated with gold nanoparticles (AuNP) and its interaction with curcumin (CUR) and gemcitabine (GEM) has been explored. Further, AuNP-BLG conjugate interactions with anticancer drugs were characterized using dynamic light scattering (DLS), zeta potential, UV-visible, Raman spectroscopy, fluorescence, circular dichroism along with molecular dynamics simulation. The cytotoxicity studies were performed using breast cancer cell lines (MCF-7). ∼8 µM of BLG resides on AuNP (∼29 nm) surface revealed by DLS. Raman scattering of AuNP-BLG conjugate showed orientation of the central calyx of BLG towards solvent. BLG fluorescence confirmed the interaction between AuNP-BLG conjugate with drugs and indicated strong binding and affinity (for CUR K_D = 3.71 x 10⁸ M ^-1, n = 1.83, and for GEM K_D = 3.78 x 10³ M ^-1, n = 0.94), enhanced in the presence of AuNP. CD and Raman analysis exhibited selective hydrophilic and hydrophobic conformations induced by drug binding. Computational studies on BLG-drug complexes revealed that the residues Pro38, Leu39 and Met107 are largely associated with CUR binding, while GEM interaction is via hydrophilic contacts which significantly matches with spectroscopic investigation. IC₅₀ values were calculated for all components of this loading system on MCF-7. The possible mechanisms of interaction between AuNP-BLG with anticancer drugs has been explored at the molecular level. We believe that these conjugates could be considered in the targeted drug delivery studies for cancer research.Communicated by Ramaswamy H. Sarma.

Simple Selection Procedure to Distinguish between Static and Flexible Loops

Loops are the most variable and unorganized elements of the secondary structure of proteins. Their ability to shift their shape can play a role in the binding of small ligands, enzymatic catalysis, or protein–protein interactions. Due to the loop flexibility, the positions of their residues in solved structures show the largest B-factors, or in a worst-case scenario can be unknown. Based on the loops’ movements’ timeline, they can be divided into slow (static) and fast (flexible). Although most of the loops that are missing in experimental structures belong to the flexible loops group, the computational tools for loop reconstruction use a set of static loop conformations to predict the missing part of the structure and evaluate the model. We believe that these two loop types can adopt different conformations and that using scoring functions appropriate for static loops is not sufficient for flexible loops. We showed that common model evaluation methods, are insufficient in the case of flexible solvent-exposed loops. Instead, we recommend using the potential energy to evaluate such loop models. We provide a novel model selection method based on a set of geometrical parameters to distinguish between flexible and static loops without the use of molecular dynamics simulations. We have also pointed out the importance of water network and interactions with the solvent for the flexible loop modeling.

Docking and Molecular Dynamics Predictions of Pesticide Binding to the Calyx of Bovine β-Lactoglobulin

Pesticides are used extensively in agriculture, and their residues in food must be monitored to prevent toxicity. The most abundant protein in cow’s milk, β-lactoglobulin (BLG), shows high affinity for diverse hydrophobic ligands in its central binding pocket, called the calyx. Several of the most frequently used pesticides are hydrophobic. To predict if BLG may be an unintended carrier for pesticides, we tested its ability to bind 555 pesticides and their isomers, for a total of 889 compounds, in a rigid docking screen. We focused on the analysis of 60 unique molecules belonging to the five pesticide classes defined by the World Health Organization, that docked into BLG’s calyx with ΔGs ranging from −8.2 to −12 kcal mol⁻¹, chosen by statistical criteria. These “potential ligands” were further analyzed using molecular dynamic simulations, and the binding energies were explored with Molecular Mechanics/Generalized Born/Surface Area (MMGBSA). Hydrophobic pyrethroid insecticides, like cypermethrin, were found to bind as deeply and tightly into the calyx as BLG’s natural ligand, palmitate; while polar compounds, like paraquat, were expelled. Our results suggest that BLG could be a carrier for pesticides, in particular for pyrethroid insecticides, allowing for their accumulation in cow’s milk beyond their solubility restrictions. This analysis opens possibilities for pesticide biosensor design based on BLG.

About TFE: Old and New Findings

The fluorinated alcohol 2,2,2-Trifluoroethanol (TFE) has been implemented for many decades now in conformational studies of proteins and peptides. In peptides, which are often disordered in aqueous solutions, TFE acts as secondary structure stabilizer and primarily induces an α -helical conformation. The exact mechanism through which TFE plays its stabilizing roles is still debated and direct and indirect routes, relying either on straight interaction between TFE and molecules or indirect pathways based on perturbation of solvation sphere, have been proposed. Another still unanswered question is the capacity of TFE to favor in peptides a bioactive or a native-like conformation rather than simply stimulate the raise of secondary structure elements that reflect only the inherent propensity of a specific amino-acid sequence. In protein studies, TFE destroys unique protein tertiary structure and often leads to the formation of non-native secondary structure elements, but, interestingly, gives some hints about early folding intermediates. In this review, we will summarize proposed mechanisms of TFE actions. We will also describe several examples, in which TFE has been successfully used to reveal structural properties of different molecular systems, including antimicrobial and aggregation-prone peptides, as well as globular folded and intrinsically disordered proteins.

Depicting the Non-Covalent Interaction of Whey Proteins with Galangin or Genistein Using the Multi-Spectroscopic Techniques and Molecular Docking

The non-covalent interactions between a commercial whey protein isolate (WPI) and two bioactive polyphenols galangin and genistein were studied at pH 6.8 via the multi-spectroscopic assays and molecular docking. When forming these WPI-polyphenol complexes, whey proteins had changed secondary structures while hydrophobic interaction was the major driving force. Detergent sodium dodecyl sulfate destroyed the hydrophobic interaction and thus decreased apparent binding constants of the WPI-polyphenol interactions. Urea led to hydrogen-bonds breakage and protein unfolding, and therefore increased apparent binding constants. Based on the measured apparent thermodynamic parameters like ΔH, ΔS, ΔG, and donor-acceptor distance, galangin with more planar stereochemical structure and random B-ring rotation showed higher affinity for WPI than genistein with location isomerism and twisted stereochemical structure. The molecular docking results disclosed that β-lactoglobulin of higher average hydrophobicity had better affinity for the two polyphenols than α-lactalbumin of lower average hydrophobicity while β-lactoglobulin possessed very similar binding sites to the two polyphenols. It is concluded that polyphenols might have different non-covalent interactions with food proteins, depending on the crucial polyphenol structures and protein hydrophobicity.

Effect of thermal and microwave processing on secondary structure of bovine β-lactoglobulin: A molecular modeling study

Milk allergy is known to cause severe allergic reactions in hypersensitive patients, especially in infants and children. β-Lactoglobulin is one of the major allergens in bovine milk. The influence of thermal and microwave processing on the structural deviations of β-lactoglobulin protein have been studied using molecular modeling techniques. The structural deviations are studied using root mean square deviations, radius of gyration, dipole moment, and solvent accessible surface area. STRIDE analysis showed significant changes in the β-lactoglobulin, especially when oscillating electric fields were applied along with heat. Root mean square fluctuations (RMSF) has been assessed for known epitopes in the β-lactoglobulin molecule. This showed that when the protein is exposed to certain thermal stress, it compacts by burying hydrophobic residues in the core. However, few allergic epitope residues also exhibit increased RMSF leading to higher reactive sites on the surface of the protein molecule. PRACTICAL APPLICATIONS: This study showed that molecular modeling can be used to gain valuable insights regarding the structural changes during processing. In the future, with more computational capacity, it can be used to make comparison between results obtained from simulations and real-time experiments. The current techniques used in food industries such as Nuclear Magnetic Resonance Imaging, Fourier Transformation Infrared Spectroscopy, X-ray diffraction can analyze pre- and post-processing effects. Hence, it become necessary to understand the changes that takes place during the processing techniques. Molecular dynamic simulation could be a useful technique in analyzing the changes occurring during the processing.

Raoult's law revisited: accurately predicting equilibrium relative humidity points for humidity control experiments

The humidity surrounding a sample is an important variable in scientific experiments. Biological samples in particular require not just a humid atmosphere but often a relative humidity (RH) that is in equilibrium with a stabilizing solution required to maintain the sample in the same state during measurements. The controlled dehydration of macromolecular crystals can lead to significant increases in crystal order, leading to higher diffraction quality. Devices that can accurately control the humidity surrounding crystals while monitoring diffraction have led to this technique being increasingly adopted, as the experiments become easier and more reproducible. Matching the RH to the mother liquor is the first step in allowing the stable mounting of a crystal. In previous work [Wheeler, Russi, Bowler & Bowler (2012). Acta Cryst. F68, 111-114], the equilibrium RHs were measured for a range of concentrations of the most commonly used precipitants in macromolecular crystallography and it was shown how these related to Raoult's law for the equilibrium vapour pressure of water above a solution. However, a discrepancy between the measured values and those predicted by theory could not be explained. Here, a more precise humidity control device has been used to determine equilibrium RH points. The new results are in agreement with Raoult's law. A simple argument in statistical mechanics is also presented, demonstrating that the equilibrium vapour pressure of a solvent is proportional to its mole fraction in an ideal solution: Raoult's law. The same argument can be extended to the case where the solvent and solute molecules are of different sizes, as is the case with polymers. The results provide a framework for the correct maintenance of the RH surrounding a sample.

Engineered β-Lactoglobulin Produced in E. coli: Purification, Biophysical and Structural Characterisation

Functional recombinant bovine β-lactoglobulin has been produced by expression in E. coli using an engineered protein gene and purified to homogeneity by applying a new protocol. Mutations L1A/I2S introduced into the protein sequence greatly facilitate in vivo cleavage of the N-terminal methionine, allowing correctly folded and soluble protein suitable for biochemical, biophysical and structural studies to be obtained. The use of gel filtration on Sephadex G75 at the last purification step enables protein without endogenous ligand to be obtained. The physicochemical properties of recombinant β-lactoglobulin such as CD spectra, ligand binding (n, K a, ΔH, TΔS, ΔG), chemical and thermal stability (ΔG D, C mid) and crystal structure confirmed that the protein obtained is almost identical to the natural one. The substitutions of N-terminal residues did not influence the binding properties of the recombinant protein so that the lactoglobulin produced and purified according to our protocol is a good candidate for further engineering and potential use in pharmacology and medicine.

Ovine β-lactoglobulin at atomic resolution

The crystal structure of the triclinic form of the milk protein β-lactoglobulin from sheep (Ovis aries) at 1.1 Å resolution is described together with a comparison of the triclinic structures of the low-pH bovine and high-pH ovine proteins. All three structures are remarkably similar, despite the well known pH-dependent conformational transition described for the bovine and porcine proteins that occurs in solution. The high resolution of the present structure determination has allowed a more accurate description of the protein than has hitherto been possible, but it is still not clear whether flexibility changes in the external loops can compensate for the presence of a significant void in the unliganded interior of the structure.

β-lactoglobulin's conformational requirements for ligand binding at the calyx and the dimer interphase: a flexible docking study

β-lactoglobulin (BLG) is an abundant milk protein relevant for industry and biotechnology, due significantly to its ability to bind a wide range of polar and apolar ligands. While hydrophobic ligand sites are known, sites for hydrophilic ligands such as the prevalent milk sugar, lactose, remain undetermined. Through the use of molecular docking we first, analyzed the known fatty acid binding sites in order to dissect their atomistic determinants and second, predicted the interaction sites for lactose with monomeric and dimeric BLG. We validated our approach against BLG structures co-crystallized with ligands and report a computational setup with a reduced number of flexible residues that is able to reproduce experimental results with high precision. Blind dockings with and without flexible side chains on BLG showed that: i) 13 experimentally-determined ligands fit the calyx requiring minimal movement of up to 7 residues out of the 23 that constitute this binding site. ii) Lactose does not bind the calyx despite conformational flexibility, but binds the dimer interface and an alternate Site C. iii) Results point to a probable lactolation site in the BLG dimer interface, at K141, consistent with previous biochemical findings. In contrast, no accessible lysines are found near Site C. iv) lactose forms hydrogen bonds with residues from both monomers stabilizing the dimer through a claw-like structure. Overall, these results improve our understanding of BLG's binding sites, importantly narrowing down the calyx residues that control ligand binding. Moreover, our results emphasize the importance of the dimer interface as an insufficiently explored, biologically relevant binding site of particular importance for hydrophilic ligands. Furthermore our analyses suggest that BLG is a robust scaffold for multiple ligand-binding, suitable for protein design, and advance our molecular understanding of its ligand sites to a point that allows manipulation to control binding.

Protein β-interfaces as a generic source of native peptide tectons

Motifs of 7-8 amino acids were designed from the β-continuous interfaces of non-related homo-oligomeric proteins. These peptides intrinsically self-assembled into nanoarchitectures in water, while retaining some properties of their parent interfaces, especially reversibility of assembly. These results reveal a novel source of native peptide tectons.

Characterization of the oligomerization and ligand-binding properties of recombinant rat lipocalin 11

Lipocalin 11 (Lcn11), a recently identified member of the lipocalin family, potentially plays crucial physiological roles in male reproduction. In this present work, we cloned, expressed and purified the rat Lcn11 (rLcn11) protein Escherichia coli. A C59A/C156A substitution was introduced to ameliorate the misfolding and aggregation problem associated with the wild-type protein. From circular dichroism and non-reducing SDS-PAGE, we characterized the conformational properties of rLcn11 as a typical lipocalin scaffold with the conserved disulfide bridge. The results obtained from size-exclusion chromatography, cross-linking experiment and dynamic light scattering analysis indicate that the recombinant rLcn11 protein forms dimer in neutral solution. By using fluorescent probe-anilino-1 napthahlene sulfonic acid (ANS), we found rLcn might contain multiple hydrophobic binding sites for ligand binding. Similarly to the odorant-binding protein, rLcn11 processes a moderate affinity for binding 1-aminoanthracene (AMA), implying that Lcn11 might work as a dimeric chemoreception protein in male reproductive.

Effect of Fructose and glucose on glycation of β-lactoglobulin in an intermediate-moisture food model system: analysis by liquid chromatography-mass spectrometry (LC-MS) and data-independent acquisition LC-MS (LC-MS(E))

To evaluate the effect of glucose and fructose on the glycation of β-lactoglobulin (β-Lg) in intermediate-moisture food (IMF), model systems consisting of β-Lg, glucose/fructose/sorbitol, glycerol, and water were established. All systems were stored at 25 and 35 °C for 2 months. The progress of the Maillard reaction and the mass change of β-Lg were investigated by the browning assay and gel electrophoresis, respectively. Meanwhile, liquid chromatography-mass spectrometry (LC-MS) and data-independent acquisition LC-MS (LC-MS(E)) were used to monitor the glycation extent and the glycated sites of β-Lg. The results indicated that glucose had a higher reaction activity of glycation than fructose, but both sugars had similar preference on the glycation site for β-Lg. The ranking order from high to low for the 9 detected glycated sites was L 1, K 91 > K 47 > K 70, K 77, K 83, K 100 > K 75 > K 135 for both sugars.

Bovine β-lactoglobulin is dimeric under imitative physiological conditions: dissociation equilibrium and rate constants over the pH range of 2.5-7.5

The oligomerization of β-lactoglobulin (βLg) has been studied extensively, but with somewhat contradictory results. Using analytical ultracentrifugation in both sedimentation equilibrium and sedimentation velocity modes, we studied the oligomerization of βLg variants A and B over a pH range of 2.5-7.5 in 100 mM NaCl at 25°C. For the first time, to our knowledge, we were able to estimate rate constants (k(off)) for βLg dimer dissociation. At pH 2.5 k(off) is low (0.008 and 0.009 s(-1)), but at higher pH (6.5 and 7.5) k(off) is considerably greater (>0.1 s(-1)). We analyzed the sedimentation velocity data using the van Holde-Weischet method, and the results were consistent with a monomer-dimer reversible self-association at pH 2.5, 3.5, 6.5, and 7.5. Dimer dissociation constants K(D)(2-1) fell close to or within the protein concentration range of ∼5 to ∼45 μM, and at ∼45 μM the dimer predominated. No species larger than the dimer could be detected. The K(D)(2-1) increased as |pH-pI| increased, indicating that the hydrophobic effect is the major factor stabilizing the dimer, and suggesting that, especially at low pH, electrostatic repulsion destabilizes the dimer. Therefore, through Poisson-Boltzmann calculations, we determined the electrostatic dimerization energy and the ionic charge distribution as a function of ionic strength at pH above (pH 7.5) and below (pH 2.5) the isoelectric point (pI∼5.3). We propose a mechanism for dimer stabilization whereby the added ionic species screen and neutralize charges in the vicinity of the dimer interface. The electrostatic forces of the ion cloud surrounding βLg play a key role in the thermodynamics and kinetics of dimer association/dissociation.

Protein-decorated reduced oxide graphene composite and its application to SERS

A globular protein, β-lactoglobulin (BLG), was used to decorate reduced graphene oxide sheets (RGO) and the obtained BLG-RGO composite can be dispersed in aqueous solution with pH-sensitive solubility. The morphology of the BLG-RGO composite was studied by transmission electron microscopy (TEM) and atomic force microscopy (AFM). The results indicate that BLG-RGO is effectively exfoliated with an average thickness of 2.5 nm. UV-vis spectra were performed to examine the reduction degree and determine the optimum concentration of β-lactoglobulin and appropriate pH value. Furthermore, Raman spectra demonstrate that β-Lactoglobulin promotes the chemical reduction process of graphene oxide and benefits to repair the crystal defects. Due to the adsorption of β-Lactoglobulin on the surface of graphene sheets, the BLG-RGO composite was further used as template for Au nanoparticles assembly. These Au nanoparticles assembled on the BLG-RGO composite were shown to yield a large SERS enhancement for Rhodamine 6G.

Structures of new crystal forms of Mycobacterium tuberculosis peptidyl-tRNA hydrolase and functionally important plasticity of the molecule

The X-ray structures of new crystal forms of peptidyl-tRNA hydrolase from M. tuberculosis reported here and the results of previous X-ray studies of the enzyme from different sources provide a picture of the functionally relevant plasticity of the protein molecule. The new X-ray results confirm the connection deduced previously between the closure of the lid at the peptide-binding site and the opening of the gate that separates the peptide-binding and tRNA-binding sites. The plasticity of the molecule indicated by X-ray structures is in general agreement with that deduced from the available solution NMR results. The correlation between the lid and the gate movements is not, however, observed in the NMR structure.

Measurement of the equilibrium relative humidity for common precipitant concentrations: facilitating controlled dehydration experiments

The dehydration of crystals of macromolecules has long been known to have the potential to increase their diffraction quality. A number of methods exist to change the relative humidity that surrounds crystals, but for reproducible results, with complete characterization of the changes induced, a precise humidity-control device coupled with an X-ray source is required. The first step in these experiments is to define the relative humidity in equilibrium with the mother liquor of the system under study; this can often be quite time-consuming. In order to reduce the time spent on this stage of the experiment, the equilibrium relative humidity for a range of concentrations of the most commonly used precipitants has been measured. The relationship between the precipitant solution and equilibrium relative humidity is explained by Raoult's law for the equilibrium vapour pressure of water above a solution. The results also have implications for the choice of cryoprotectant and solutions used to dehydrate crystals. For the most commonly used precipitants (10-30% PEG 2000-8000), the starting point will be a relative humidity of 99.5%.

Structure and stability of Gyuba, a β-lactoglobulin chimera

β-lactoglobulin (LG) contains nine β-strands (strands A-I) and one α-helix. Strands A-H form a β-barrel. At neutral pH, equine LG (ELG) is monomeric, whereas bovine LG (BLG) is dimeric, and the I-strands of its two subunits form an intermolecular β-sheet. We previously constructed a chimeric ELG in which the sequence of the I-strand was replaced with that of BLG. This chimera did not dimerize. For this study, we constructed the new chimera we call Gyuba (which means cow and horse in Japanese). The amino acid sequence of Gyuba includes the sequences of the BLG secondary structures and those of the ELG loops. The crystal structure of Gyuba is very similar to that of BLG and indicates that Gyuba dimerizes via the intermolecular β-sheet formed by the two I-strands. Thus, the entire arrangement of the secondary structural elements is important for LG dimer formation.

A few low-frequency normal modes predominantly contribute to conformational responses of hen egg white lysozyme in the tetragonal crystal to variations of molecular packing controlled by environmental humidity

The structures of proteins in crystals are fixed by molecular interactions with neighboring molecules, except in non-contacting flexible regions. Thus, it is difficult to imagine what conformational changes occur in solution. However, if molecular interactions can be changed by manipulating molecular packing in crystals, it may be possible to visualize conformational responses of proteins at atomic resolution by diffraction experiments. For this purpose, it is suitable to control the molecular packing in protein crystals by changing the volume of solvent channels through variation of the environmental relative humidity. Here, we studied conformational responses of hen egg white lysozyme (HEWL) in the tetragonal crystal by X-ray diffraction experiments using a humidity-control apparatus, which provided air flow of 20-98%rh at 298 K. First, we monitored the lattice parameters and crystalline order during dehydration and rehydration of HEWL crystal between 61 and 94%rh at 300 K. Then two crystal structures at a resolution of 2.1 Å using diffraction data obtained at 84.2 and 71.9%rh were determined to discuss the conformational responses of HEWL against the external perturbation induced by changes in molecular packing. The structure at 71.9%rh displayed a closure movement that was likely induced by the molecular contacts formed during dehydration and could be approximated by ten low-frequency normal modes for the crystal structure obtained at 84.2%rh. In addition, we observed reorganization of hydration structures at the molecular interfaces between symmetry neighbors. These findings suggest that humidity-controlled X-ray crystallography is an effective tool to investigate the responses of inherent intramolecular motions of proteins to external perturbations.

Structural ordering of disordered ligand-binding loops of biotin protein ligase into active conformations as a consequence of dehydration

Mycobacterium tuberculosis (Mtb), a dreaded pathogen, has a unique cell envelope composed of high fatty acid content that plays a crucial role in its pathogenesis. Acetyl Coenzyme A Carboxylase (ACC), an important enzyme that catalyzes the first reaction of fatty acid biosynthesis, is biotinylated by biotin acetyl-CoA carboxylase ligase (BirA). The ligand-binding loops in all known apo BirAs to date are disordered and attain an ordered structure only after undergoing a conformational change upon ligand-binding. Here, we report that dehydration of Mtb-BirA crystals traps both the apo and active conformations in its asymmetric unit, and for the first time provides structural evidence of such transformation. Recombinant Mtb-BirA was crystallized at room temperature, and diffraction data was collected at 295 K as well as at 120 K. Transfer of crystals to paraffin and paratone-N oil (cryoprotectants) prior to flash-freezing induced lattice shrinkage and enhancement in the resolution of the X-ray diffraction data. Intriguingly, the crystal lattice rearrangement due to shrinkage in the dehydrated Mtb-BirA crystals ensued structural order of otherwise flexible ligand-binding loops L4 and L8 in apo BirA. In addition, crystal dehydration resulted in a shift of approximately 3.5 A in the flexible loop L6, a proline-rich loop unique to Mtb complex as well as around the L11 region. The shift in loop L11 in the C-terminal domain on dehydration emulates the action responsible for the complex formation with its protein ligand biotin carboxyl carrier protein (BCCP) domain of ACCA3. This is contrary to the involvement of loop L14 observed in Pyrococcus horikoshii BirA-BCCP complex. Another interesting feature that emerges from this dehydrated structure is that the two subunits A and B, though related by a noncrystallographic twofold symmetry, assemble into an asymmetric dimer representing the ligand-bound and ligand-free states of the protein, respectively. In-depth analyses of the sequence and the structure also provide answers to the reported lower affinities of Mtb-BirA toward ATP and biotin substrates. This dehydrated crystal structure not only provides key leads to the understanding of the structure/function relationships in the protein in the absence of any ligand-bound structure, but also demonstrates the merit of dehydration of crystals as an inimitable technique to have a glance at proteins in action.

Water-mediated variability in the structure of relaxed-state haemoglobin

The crystal structure of high-salt horse methaemoglobin has been determined at environmental relative humidities (r.h.) of 88, 79, 75 and 66%. The molecule is in the R state in the native and the r.h. 88% crystals. At r.h. 79%, the water content of the crystal is reduced and the molecule appears to move towards the R2 state. The crystals undergo a water-mediated transformation involving a doubling of one of the unit-cell parameters and an increase in water content when the environmental humidity is further reduced to r.h. 75%. The water content is now similar to that in the native crystals and the molecules are in the R state. The crystal structure at r.h. 66% is similar, but not identical, to that at r.h. 75%, but the solvent content is substantially reduced and the molecules have a quaternary structure that is in between those corresponding to the R and R2 states. Thus, variation in hydration leads to variation in the quaternary structure. Furthermore, partial dehydration appears to shift the structure from the R state to the R2 state. This observation is in agreement with the earlier conclusion that the changes in protein structure that accompany partial dehydration are similar to those that occur during protein action.