Tryptophan-19 of beta-lactoglobulin, the only residue completely conserved in the lipocalin superfamily, is not essential for binding retinol, but relevant to stabilizing bound retinol and maintaining its structure

Variability in phenylalanine side chain conformations facilitates broad substrate tolerance of fatty acid binding in cockroach milk proteins

Diploptera punctata, also known as the Pacific beetle cockroach, is a viviparous cockroach that gives birth to live offspring and secretes a highly concentrated mixture of glycosylated proteins as a source of nourishment for developing embryos. These proteins are lipocalins that bind to lipids and crystallize in the gut of the embryo. A structure of milk crystals harvested from the embryos showed that the milk-derived crystals were heterogeneous and made of three proteins (called Lili-Mips). We hypothesized that the isoforms of Lili-Mip would display different affinities for fatty acids due to the ability of the pocket to bind multiple acyl chain lengths. We previously reported the structures of Lili-Mip from crystals grown in vivo and recombinantly expressed Lili-Mip2. These structures are similar, and both bind to several fatty acids. This study explores the specificity and affinity of fatty acid binding to recombinantly expressed Lili-Mip 1, 2 & 3. We show that all isoforms can bind to different fatty acids with similar affinities. We also report the thermostability of Lili-Mip is pH dependent, where stability is highest at acidic pH and declines as the pH increases to physiological levels near 7.0. We show that thermostability is an inherent property of the protein, and glycosylation and ligand binding do not change it significantly. Measuring the pH in the embryo's gut lumen and gut cells suggests that the pH in the gut is acidic and the pH inside the gut cells is closer to neutral pH. In various crystal structures (reported here and previously by us), Phe-98 and Phe-100 occupy multiple conformations in the binding pocket. In our earlier work, we had shown that the loops at the entrance could adapt various conformations to change the size of the binding pocket. Here we show Phe-98 and Phe-100 can reorient to stabilize interactions at the bottom of the cavity-and change the volume of the cavity from 510 Å3 to 337 Å3. Together they facilitate the binding of fatty acids of different acyl chain lengths.

A 200 nanoseconds all-atom simulation of the pH-dependent EF loop transition in bovine β-lactoglobulin. The role of the orientation of the E89 side chain

In silico molecular dynamics (MD) using crystallographic and NMR data was used to simulate the effects of the protonation state of E89 on the pH-dependent conformational rearrangement of the EF loop, also known as the Tanford transition, in a series of apo-β-lactoglobulin (BLG) structures. Compared to existing studies these simulations were carried out over a much longer time scale (200 ns where the stability of the transition can be evaluated) and used an explicit water model. We considered eight different entries from the Brookhaven Protein Data Bank (PDB) separated into two groups. We observed that fixing the protonation state of E89 prompts the transition of the EF loop only when its side chain is oriented under the loop and into the entrance of the interior cavity. The motion of the EF loop occurs mostly as a step-function and its timing varies greatly from ∼ 20 ns to ∼170 ns from the beginning of the simulation. Once the transition is completed, the protein appears to reach a stable conformation as in a true two-state transition. We also observed novel findings. When the transition occurs, the hydrogen bond between E89 and S116 is replaced with a salt bridge with Lys residues in the βC-CD loop-βD motif. This electrostatic interaction causes the distortion of this motif as well as the protrusion of the GH loop into the aperture of the cavity with the result of limiting the increase of its contour area despite the rotation of the EF loop.Communicated by Ramaswamy H. Sarma.

Structure-based design approach to rational site-directed mutagenesis of β-lactoglobulin

Recombinant proteins play an important role in medicine and have diverse applications in industrial biotechnology. Lactoglobulin has shown great potential for use in targeted drug delivery and body fluid detoxification because of its ability to bind a variety of molecules. In order to modify the biophysical properties of β-lactoglobulin, a series of single-site mutations were designed using a structure-based approach. A 3-dimensional structure alignment of homologous molecules led to the design of nine β-lactoglobulin variants with mutations introduced in the binding pocket region. Seven stable and correctly folded variants (L39Y, I56F, L58F, V92F, V92Y, F105L, M107L) were thoroughly characterized by fluorescence, circular dichroism, isothermal titration calorimetry, size-exclusion chromatography, and X-ray structural investigations. The effects of the amino acid substitutions were observed as slight rearrangements of the binding pocket geometry, but they also significantly influenced the global properties of the protein. Most of the mutations increased the thermal/chemical stability without altering the dimerization constant or pH-dependent conformational behavior. The crystal structures reveal that the I56F and F105L mutations reduced the depth of the binding pocket, which is advantageous since it can reduce the affinity to endogenous fatty acids. The F105L mutant created a unique binding mode for a fatty acid, supporting the idea that lactoglobulin can be altered to bind unique molecules. Selected variants possessing a unique combination of their individual properties can be used for further, more advanced mutagenesis, and the presented results support further research using β-lactoglobulin as a therapeutic delivery agent or a blood detoxifying molecule.

Surface patch binding induced interaction of anisotropic nanoclays with globular plasma proteins

Morphology dependent interaction of model anisotropic nanoparticles with globular plasma proteins.

Crystal structures of three representatives of a new Pfam family PF14869 (DUF4488) suggest they function in sugar binding/uptake

Crystal structures of three members (BACOVA_00364 from Bacteroides ovatus, BACUNI_03039 from Bacteroides uniformis and BACEGG_00036 from Bacteroides eggerthii) of the Pfam domain of unknown function (DUF4488) were determined to 1.95, 1.66, and 1.81 Å resolutions, respectively. The protein structures adopt an eight-stranded, calycin-like, β-barrel fold and bind an endogenous unknown ligand at one end of the β-barrel. The amino acids interacting with the ligand are not conserved in any other protein of known structure with this particular fold. The size and chemical environment of the bound ligand suggest binding or transport of a small polar molecule(s) as a potential function for these proteins. These are the first structural representatives of a newly defined PF14869 (DUF4488) Pfam family.

A small variance in the antigenicity but not function of recombinant β-lactoglobulin purified from the culture supernatant of transformed yeast cells

We purified recombinant bovine β-lactoglobulin (rβ-LG) from the culture supernatant of transformed yeast and investigated whether rβ-LG maintained the functional ability and antigenicity of native β-LG. Immunostaining following gel electrophoresis and reversed-phase high-performance liquid chromatography confirmed that rβ-LG was purified homogeneously. rβ-LG showed almost the same retinol-binding ability as native β-LG purified from bovine milk. However, affinities of two anti-β-LG monoclonal antibodies (mAbs) to rβ-LG were different from those to native β-LG, although three other mAbs bound these two proteins equally. Since our panel of five mAbs has been previously shown to be able to detect structural changes occurring in β-LG, this variance in antigenicity can be attributed to conformational differences between rβ-LG and native β-LG. Then, we studied which step in the production and purification procedure was responsible for altering the antigenicity of rβ-LG. Bovine milk native β-LG was added to several steps in this procedure and purified in the same manner as rβ-LG. The results suggested that incubation in the yeast culture had adverse effects on maintaining the antigenicity of this recombinant protein. We conclude from these results that even if no difference between the native and recombinant proteins can be detected by functional analysis, some subtle conformational change which can be distinguished by mAbs may be incorporated into the recombinant protein during its production and ultimately cause a different immune reaction in vivo.Abbreviations β-LG, β-lactoglobulin; rβ-LG, recombinant β-LG; PBS, phosphate-buffered saline; PBS-Tween, PBS containing 0.05% Tween 20; ELISA, enzyme-linked immunosorbent assay.

NMR structure of lipoprotein YxeF from Bacillus subtilis reveals a calycin fold and distant homology with the lipocalin Blc from Escherichia coli

The soluble monomeric domain of lipoprotein YxeF from the Gram positive bacterium B. subtilis was selected by the Northeast Structural Genomics Consortium (NESG) as a target of a biomedical theme project focusing on the structure determination of the soluble domains of bacterial lipoproteins. The solution NMR structure of YxeF reveals a calycin fold and distant homology with the lipocalin Blc from the Gram-negative bacterium E.coli. In particular, the characteristic β-barrel, which is open to the solvent at one end, is extremely well conserved in YxeF with respect to Blc. The identification of YxeF as the first lipocalin homologue occurring in a Gram-positive bacterium suggests that lipocalins emerged before the evolutionary divergence of Gram positive and Gram negative bacteria. Since YxeF is devoid of the α-helix that packs in all lipocalins with known structure against the β-barrel to form a second hydrophobic core, we propose to introduce a new lipocalin sub-family named ‘slim lipocalins’, with YxeF and the other members of Pfam family PF11631 to which YxeF belongs constituting the first representatives. The results presented here exemplify the impact of structural genomics to enhance our understanding of biology and to generate new biological hypotheses.

Cation-π interactions in lipocalins: structural and functional implications

The cation-π interaction impacts protein folding, structural stability, specificity, and molecular recognition. Cation-π interactions have been overlooked in the lipocalin family. To fill this gap, these interactions were analyzed in the 113 crystal and solution structures from the lipocalin family. The cation-π interactions link previously identified structurally conserved regions and reveal new motifs, which are beyond the reach of a sequence alignment algorithm. Functional and structural significance of the interactions were tested experimentally in human tear lipocalin (TL). TL, a prominent and promiscuous lipocalin, has a key role in lipid binding at the ocular surface. Ligand binding modulation through the loop AB at the "open" end of the barrel has been erroneously attributed solely to electrostatic interactions. Data revealed that the interloop cation-π interaction in the pair Phe28-Lys108 contributes significantly to stabilize the holo-conformation of the loop AB. Numerous energetically significant and conserved cation-π interactions were uncovered in TL and throughout the lipocalin family. Cation-π interactions, such as the highly conserved Trp17-Arg118 pair in TL, were educed in low temperature experiments of mutants with Trp to Tyr substitutions.

Bound fatty acids modulate the sensitivity of bovine β-lactoglobulin to chemical and physical denaturation

Fatty acids are the natural ligands associated with the bovine milk lipocalin, β-lactoglobulin (BLG), and were identified by means of mass spectrometry. The naturally bound ligands were found to contribute to the stability of the proteins toward denaturation by both temperature and chaotropes. To assess the nature of the structural regions involved in this stabilization, the thermodynamic and kinetic aspects of the stability of various structural regions of the proteins were studied in the presence of bound palmitate, which is the most abundant natural ligand. Binding of a single palmitate molecule was found to affect not only the stability of the calyx region, where palmitate is bound, but also that of the region at the hydrophobic interface between the barrel itself and the long helix in the protein structure, where the thiol group of Cys121 is buried. This region is known to be essential for the stability of the BLG dimer and is relevant to the generation of "reactive monomers" that are involved in covalent and noncovalent polymerization of BLG and in the formation of covalent adducts with other milk proteins.

Molecular interactions of the neuronal GPI-anchored lipocalin Lazarillo

Lazarillo, a glycoprotein involved in axon growth and guidance in the grasshopper embryo, is the only member of the lipocalin family that is attached to the cell surface by a GPI anchor. Recently, the study of Lazarillo homologous genes in Drosophila and mouse has revealed new functions in the regulation of lifespan, stress resistance and neurodegeneration. Here we report an analysis of biochemical properties of Lazarillo to gain insight into the molecular basis of its physiological function. Recombinant forms of the grasshopper protein were expressed in two different systems to test: (1) potential binding of several hydrophobic ligands; (2) protein-protein homophilic interactions; and (3) whether interaction with the function-blocking mAb 10E6 interferes with ligand binding. We tested 10 candidate ligands (retinoic acid, heme, bilirubin, biliverdin, ecdysterone, juvenile hormone, farnesol, arachidonic acid, linoleic acid and palmitic acid), and monitored binding using electrophoretic mobility shift, absorbance spectrum, and fluorimetry assays. Our work indicates binding to heme and retinoic acid, resulting in increased electrophoretic mobility, as well as to fatty acids, resulting in multimerization. Retinoic acid and fatty acids binding were confirmed by fluorescence titration, and heme binding was confirmed with absorbance spectrum assays. We demonstrate that Lazarillo oligomerizes in solution and can form clusters in the plasma membrane when expressed and GPI-anchored to the cell surface, however it is unable to mediate cell-cell adhesion. Finally, by ligand-mAb competition experiments we show that ligand-binding alone cannot be the key factor for Lazarillo to perform its function during axonal growth in the grasshopper embryo.

Distantly related lipocalins share two conserved clusters of hydrophobic residues: use in homology modeling

Background

Lipocalins are widely distributed in nature and are found in bacteria, plants, arthropoda and vertebra. In hematophagous arthropods, they are implicated in the successful accomplishment of the blood meal, interfering with platelet aggregation, blood coagulation and inflammation and in the transmission of disease parasites such as Trypanosoma cruzi and Borrelia burgdorferi.

The pairwise sequence identity is low among this family, often below 30%, despite a well conserved tertiary structure. Under the 30% identity threshold, alignment methods do not correctly assign and align proteins. The only safe way to assign a sequence to that family is by experimental determination. However, these procedures are long and costly and cannot always be applied. A way to circumvent the experimental approach is sequence and structure analyze. To further help in that task, the residues implicated in the stabilisation of the lipocalin fold were determined. This was done by analyzing the conserved interactions for ten lipocalins having a maximum pairwise identity of 28% and various functions.

Results

It was determined that two hydrophobic clusters of residues are conserved by analysing the ten lipocalin structures and sequences. One cluster is internal to the barrel, involving all strands and the 3₁₀ helix. The other is external, involving four strands and the helix lying parallel to the barrel surface. These clusters are also present in RaHBP2, a unusual "outlier" lipocalin from tick Rhipicephalus appendiculatus. This information was used to assess assignment of LIR2 a protein from Ixodes ricinus and to build a 3D model that helps to predict function. FTIR data support the lipocalin fold for this protein.

Conclusion

By sequence and structural analyzes, two conserved clusters of hydrophobic residues in interactions have been identified in lipocalins. Since the residues implicated are not conserved for function, they should provide the minimal subset necessary to confer the lipocalin fold. This information has been used to assign LIR2 to lipocalins and to investigate its structure/function relationship. This study could be applied to other protein families with low pairwise similarity, such as the structurally related fatty acid binding proteins or avidins.

Selective modification of Trp19 in beta-lactoglobulin by a new diazo fluorescence probe

To obtain the local information on the tryptophan domain in a protein, the design and synthesis of a new fluorescent probe, 1,7-bis(4-hydroxy-3-methoxyphenyl)-4-diazo-1,6-heptadiene-3,5-dione, is reported for the selective modification of tryptophan residues. The probe comprises a curcumin fluorophore and a diazo labeling group, whose spectroscopic properties are characterized. The diazo group may be catalytically degraded by transition metal complexes such as Rh2(OAc)4, generating an active rhodium carbenoid intermediate, which can react selectively with tryptophan residues. By the use of the carbene's intermolecular reactions, the tryptophan residue (Trp19) of beta-lactoglobulin may be modified with the diazo curcumin probe. Furthermore, slight secondary but larger tertiary structural changes are detected after Trp19 is modified, and the Trp19 modification produces a great effect on the binding of 8-anilino-1-naphthalenesulfonic acid and retinol. These results indicate that the Trp19 residue plays an essential role in the structure and stability of beta-lactoglobulin, and the specific modification of this residue may have a potential use in further elucidating the relationship between the structure and function of the protein.

A Tryptophan Rotamer Located in a Polar Environment Probes pH-Dependent Conformational Changes in Bovine β-Lactoglobulin A

Bovine beta-lactoglobulin A (BLGA) is a well characterized globular protein whose tertiary structure has been investigated in detail. BLGA undergoes a pH-dependent conformational change which X-ray data described as involving mostly the loop connecting strands E and F and the deprotonation of a glutamic acid residue (Glu89). These structural changes have been investigated using, among other techniques, fluorescence spectroscopy. The intrinsic fluorescence of BLGA is dominated by two Trp residues. These residues are located far from the EF loop and would not be expected to probe the pH-induced conformational change of the protein. Trp19 is located at the bottom of the interior beta-barrel, whereas Trp61 is located at the aperture of the barrel near the CD loop and is "silent" in the emission of native BLGA because of the proximity of a disulfide moiety. Our study suggests that, surprisingly, the fluorescence of Trp19 has the characteristic of a more polar environment than structural models from X-ray data would suggest and that at least two distinct conformations (or rotamers) of Trp19 contribute to the fluorescence of the protein. The less populated rotamer (relative amplitude (alpha) approximately 20%, tau approximately 3 ns) probes a more polar environment and a pH-dependent conformational change of BLGA in the region of Trp19 which X-ray data do not detect. Finally, our study provides the estimate of the fluorescence lifetime of Trp61 in the "unquenched" form.

The pH-dependent conformational transition of β-lactoglobulin modulates the binding of protoporphyrin IX

We have investigated the interaction between PPIX and beta-lactoglobulin (beta-lg) as a function of the pH of the solution. beta-lg is a small globular protein (MW approximately 18 kDa) with a very well characterized structure that reveals several possible binding sites for ligands. The interaction with beta-lg affects the photophysical properties of PPIX. The shift of PPIX emission maximum, excitation maximum and the increase of the fluorescence intensity is an indicator that binding between the porphyrin and beta-lg occurs. The binding constant appears to be modulated by the pH of the solution. Spectroscopic measurements do not reveal any significant energy transfer between the Trp residues of beta-lg and PPIX, however, fluorescence anisotropy decay measurements confirm the binding and the modulation introduced by the pH of the solution. Since beta-lg has been shown to be stable within the range of pH adopted in our experiments (5.0-9.0), the results suggest that PPIX binds a site affected by the pH of the solution. Because of the crystallographic evidence an obvious site is near the aperture of the interior beta-barrel however an alternative (or concurrent) binding site may still be present.

Large-scale prediction of protein geometry and stability changes for arbitrary single point mutations

We have developed a method to both predict the geometry and the relative stability of point mutants that may be used for arbitrary mutations. The geometry optimization procedure was first tested on a new benchmark of 2141 ordered pairs of X-ray crystal structures of proteins that differ by a single point mutation, the largest data set to date. An empirical energy function, which includes terms representing the energy contributions of the folded and denatured proteins and uses the predicted mutant side chain conformation, was fit to a training set consisting of half of a diverse set of 1816 experimental stability values for single point mutations in 81 different proteins. The data included a substantial number of small to large residue mutations not considered by previous prediction studies. After removing 22 (approximately 2%) outliers, the stability calculation gave a standard deviation of 1.08 kcal/mol with a correlation coefficient of 0.82. The prediction method was then tested on the remaining half of the experimental data, giving a standard deviation of 1.10 kcal/mol and covariance of 0.66 for 97% of the test set. A regression fit of the energy function to a subset of 137 mutants, for which both native and mutant structures were available, gave a prediction error comparable to that for the complete training set with predicted side chain conformations. We found that about half of the variation is due to conformation-independent residue contributions. Finally, a fit to the experimental stability data using these residue parameters exclusively suggests guidelines for improving protein stability in the absence of detailed structure information.

Epitopic characterization of native bovine beta-lactoglobulin

Two monoclonal antibodies (mAbs) (mAb 97 and mAb 117) selected from a panel of 52 mAbs directed against beta-lactoglobulin (BLG) have previously been used to develop a two-site enzyme immunometric assay (EIA) specific for the native form of the protein [J. Immunol. Methods 220 (1998) 25]. In the present work, the conformational epitopes recognized by these two mAbs and by the 50 others have been studied. Firstly, an epitope map was drawn using a surface plasmon resonance (SPR) biosensor: the epitopes were organized in a circle of 11 overlapping and 1 nonoverlapping antigenic regions. Secondly, 55 site-directed BLGA mutants were prepared and tested by ELISA and competitive immunoassay to localize these 12 antigenic regions on the protein molecule. Among them, 20 mutants showed a 10- to 7500-fold decrease in relative affinity for the mAbs of one or several neighbouring regions: their circular dichroism (CD) spectra were identical to the spectrum of wild-type (WT) BLGA. At least one mutant was found for each of the 11 overlapping antigenic regions which circled the molecule and for the nonoverlapping one which was localized near the entrance of the calyx. The two mAbs initially chosen were each directed towards very conformation-dependent epitopes and were thus suitable for monitoring native BLG in food products and manufacturing processes. Other mAb pairs could be used to follow the fate of specific regions of the molecule during denaturation or proteolytic digestion.

RET and anisotropy measurements establish the proximity of the conserved Trp17 to Ile98 and Phe99 of tear lipocalin

Previous studies suggest that the conserved Trp17 on strand A of TL has a role in lipocalin stability and interacts, directly or indirectly, with Ile98 and Phe99 on strand G to influence ligand binding. Here, we determined the proximity of Trp17 to Ile98 and Phe99. Time-resolved fluorescence experiments showed resonance energy transfer between tryptophans at positions 17 and 98. In addition, an exciton effect was discovered in CD experiments resulting from interactions of the excited states of these tryptophans. Fluorescence anisotropy values of mutants containing two tryptophans (positions 99/17 and 98/17) were lower than expected in the absence of RET, confirming that these residues are proximate in tear lipocalin. The data support a model of tear lipocalin in which Trp17 and Phe99 are close together deep in the cavity and participate in an internal hydrophobic cluster. Ile98 is proximate to Trp17 but faces toward the outside of the cavity and in the model is part of an external hydrophobic patch. Comparison with beta-lactoglobulin suggests that these motifs may have an important influence on protein stability and ligand binding in other members of the lipocalin family.

The ligand-binding site of bovine beta-lactoglobulin: evidence for a function?

Ever since the fortuitous observation that beta-lactoglobulin (beta-Lg), the major whey protein in the milk of ruminants, bound retinol, the details of the binding have been controversial. beta-Lg is a lipocalin, like plasma retinol-binding protein, so that ligand association was expected to make use of the central cavity in the protein. However, an early crystallographic analysis and some of the more recent solution studies indicated binding elsewhere. We have now determined the crystal structures of the complexes of the trigonal form of beta-Lg at pH 7.5 with bound retinol (R=21.4% for 7329 reflections between 20 and 2.4 A resolution, R(free)=30.6%) and with bound retinoic acid (R=22.7% for 7813 reflections between 20 and 2.34 A resolution, R(free)=29.8%). Both ligands are found to occupy the central calyx in a manner similar to retinol binding in retinol-binding protein. We find no evidence of binding at the putative external binding site in either of these structural analyses. Further, competition between palmitic acid and retinol reveals only palmitate bound to the protein. An explanation is provided for the lack of ligand binding to the orthorhombic crystal form also obtained at pH 7.5. Finally, the possible function of beta-Lg is discussed in the light of its species distribution and similarity to other lipocalins.

Role of conserved residues in structure and stability: tryptophans of human serum retinol-binding protein, a model for the lipocalin superfamily

Serum retinol binding protein (RBP) is a member of the lipocalin family, proteins with up-and-down beta-barrel folds, low levels of sequence identity, and diverse functions. Although tryptophan 24 of RBP is highly conserved among lipocalins, it does not play a direct role in activity. To determine if Trp24 and other conserved residues have roles in stability and/or folding, we investigated the effects of conservative substitutions for the four tryptophans and some adjacent residues on the structure, stability, and spectroscopic properties of apo-RBP. Crystal structures of recombinant human apo-RBP and of a mutant with substitutions for tryptophans 67 and 91 at 1.7 A and 2.0 A resolution, respectively, as well as stability measurements, indicate that these relatively exposed tryptophans have little influence on structure or stability. Although Trp105 is largely buried in the wall of the beta-barrel, it can be replaced with minor effects on stability to thermal and chemical unfolding. In contrast, substitutions of three different amino acids for Trp24 or replacement of Arg139, a conserved residue that interacts with Trp24, lead to similar large losses in stability and lower yields of native protein generated by in vitro folding. The results and the coordinated nature of natural substitutions at these sites support the idea that conserved residues in functionally divergent homologs have roles in stabilizing the native relative to misfolded structures. They also establish conditions for studies of the kinetics of folding and unfolding by identifying spectroscopic signals for monitoring the formation of different substructures.

Plant lipocalins: violaxanthin de-epoxidase and zeaxanthin epoxidase

Violaxanthin de-epoxidase and zeaxanthin epoxidase catalyze the interconversions between the carotenoids violaxanthin, antheraxanthin and zeaxanthin in plants. These interconversions form the violaxanthin or xanthophyll cycle that protects the photosynthetic system of plants against damage by excess light. These enzymes are the first reported lipocalin proteins identified from plants and are only the second examples of lipocalin proteins with enzymatic activity. This review summarizes the discovery and characterization of these two unique lipocalin enzymes and examines the possibility of other potential plant lipocalin proteins.

Solution structure of a recombinant mouse major urinary protein

Major urinary proteins (MUPs) form an ensemble of protein isoforms which are expressed and secreted by sexually mature male mice only. They belong to the lipocalin superfamily and share with other members of this family the capacity to bind hydrophobic molecules, some of which are odorants. MUPs, either associated with or free of their natural ligands, play an important role in the reproductive cycle of these rodents by acting as pheromones. In fact, they are able to interact with receptors in the vomeronasal organ of the female mice, inducing hormonal and physiological responses by an as yet unknown mechanism. In order to investigate the structural and dynamical features of these proteins in solution, one of the various wild-type isoforms (rMUP: 162 residues) was cloned and subsequently isotopically labeled. The complete 1H, 13C and 15N resonance assignment of that isoform, achieved by using a variety of multidimensional heteronuclear NMR experiments, has been reported recently. Here, we describe the refined high-resolution three-dimensional solution structure of rMUP in the native state, obtained by a combination of distance geometry and energy minimization calculations based on 2362 NOE-derived distance restraints. A comparison with the crystal structure of the wild-type MUPs reveals, aside from minor differences, a close resemblance in both secondary structure and overall topology. The secondary structure of the protein consists of eight antiparallel beta-strands forming a single beta-sheet and an alpha-helix in the C-terminal region. In addition, there are several helical and hairpin turns distributed throughout the protein sequence, mostly connecting the beta-strands. The tertiary fold of the beta-sheet creates a beta-barrel, common to all members of the lipocalin superfamily. The shape of the beta-barrel resembles a calyx, lined inside by mostly hydrophobic residues that are instrumental for the binding and transport of small nonpolar ligand molecules.

Binding studies of tear lipocalin: the role of the conserved tryptophan in maintaining structure, stability and ligand affinity

The principal lipid binding protein in tears, tear lipocalin (TL), binds acid and the fluorescent fatty acid analogs, DAUDA and 16-AP at one site TL compete for this binding site. A fluorescent competitive binding assay revealed that apo-TL has a high affinity for phospholipids and stearic acid (Ki) of 1.2 microM and 1.3 microM, respectively, and much less affinity for cholesterol (Ki) of 15.9 of the hydrocarbon chain. TL binds most strongly the least soluble lipids permitting these lipids to exceed their maximum solubility in aqueous solution. These data implicate TL in solubilizing and transporting lipids in the tear film. Phenylalanine, tyrosine and cysteine+ were substituted for TRP 17, the only invariant residue throughout the lipocalin superfamily. Cysteine substitution resulted in some loss os secondary structure, relaxation of aromatic side chain rigidity, decreased binding affinity for DAUDA and destabilization of structure. Mutants of TL, W17Y, and W17F showed a higher binding affinity for DAUDA than wild-type TL. Comparison of the results of the tryptophan 17 substitution in lipocalin with those of tryptophan 19 substitution in beta-lactoglobulin revealed important differences in binding characteristics that reflect the functional heterogeneity within the lipocalin family.

Accelerated secretion of mutant beta-lactoglobulin in Saccharomyces cerevisiae resulting from a single amino acid substitution

Transformed yeasts producing a mutant form of bovine beta-lactoglobulin (beta-LG), W19Y, in which Trp(19) was replaced with Tyr, were shown to secrete 6 times more than those producing wild type beta-LG. Northern blot analysis suggested that the enhanced level of secretion was not the result of upregulated transcription of W19Y. The ratio of the amount of W19Y secreted into the supernatant to the amount of W19Y remaining inside the cells was much larger than that in the case of wild type beta-LG as shown by immunoblot analysis. A pulse/chase experiment revealed that the speed of secretion of W19Y was significantly accelerated, compared to wild type beta-LG. These results indicated that W19Y was more efficiently and rapidly transported in the course of secretion than wild type beta-LG. Our previous study showed that the DeltaG of unfolding of W19Y in water is 6.9 kcal/mol smaller than that of wild type beta-LG. Furthermore, immunoblot analysis of intracellular beta-LG under non-reducing conditions indicated that W19Y as well as wild type beta-LG maintained a specific folded structure inside the yeast cells, whereas other non-secretable mutant beta-LGs with Phe or Ala at position 19 (W19F and W19A, respectively) did not. These data suggest that low molecular stability and the maintenance of a specific folded structure inside the yeast cells are prerequisites for efficient and rapid secretion. W19Y was more efficiently secreted than wild type beta-LG also in transformed ern1 mutant yeast cells expressing only a basal level of BiP which is considered to function in quality control in the endoplasmic reticulum (ER) by playing an important role in determining the secretion efficiency of secretory proteins. Thus, the reason for the enhanced secretion of W19Y is considered to be that the improved folding ability of W19Y can allow the half-life of the W19Y-BiP complex to become shorter than that of the wild type beta-LG-BiP complex, leading to faster translocation of W19Y into transport vesicles, or that W19Y can fold in a BiP-independent manner in the ER of the yeast cells. Our findings demonstrate that the amount of protein secreted can be improved by alteration of a single amino acid residue crucial for its structure.

Physico-chemical characterization of human von Ebner gland protein expressed in Escherichia coli: implications for its physiological role

The human von Ebner gland protein (VEG) was expressed in Escherichia coli and purified to homogeneity. The sequence and mass of the recombinant protein were confirmed, and far and near UV circular dichroic analyses showed that the protein was properly folded. The secondary structure of recombinant VEG consisted of 75% beta-sheets and 12% alpha-helices, and it was found to be stable under acidic conditions, in the presence of alcohol, and at high temperatures. The denaturation temperature was 79 degreesC at pH 3.5, with a denaturation enthalpy (DeltaHd) of 160,600 J/mol. Fluorescence analysis and measurement of the denaturation temperature by circular dichroism did not detect any interaction between VEG and extremely bitter (denatonium benzoate, caffein) or sweet (aspartame) compounds. These results suggest that VEG may not function as a shuttle for transfer of sapid molecules to taste receptors.

Structural changes in human tear lipocalins associated with lipid binding

Structural and conformational changes in tear lipocalins were detected in association with ligand binding and release. Circular dichroism measurements demonstrated that ligand binding induces beta structure formation, aromatic side chain asymmetry, and a more rigid state in tear lipocalins (TL). The exposure of the tyrosyl component is less in apo-TL than in holo-TL. The sole tryptophan residue, Trp17, is buried in both holo- and apo-TL. The steady state exposure of Trp17 is the same in holo- and apo-TL, but the dynamic exposure is two-fold greater in apo-TL. Maneuvers to unfold the protein with urea or incubation in an acidic environment resulted in increased exposure of aromatic amino acids. Electron paramagnetic resonance studies verified that lipids are liberated from TL in an acidic environment. Acidic pH promotes conformational changes in TL involving aromatic residues, particularly the conserved residue Trp17. These changes are associated with lipid release. The liberation of lipid from the cavity of TL under acidic conditions involves a molten globule state of the protein. We postulate that TL, exposed to the steep surface pH gradient that exists at lipid-aqueous interfaces, would release lipid in association with a molten globule transition. The data suggest a plausible regulatory mechanism for lipid delivery from lipocalins at the tear film surface.

Identification of a conserved hydrophobic cluster in partially folded bovine beta-lactoglobulin at pH 2

BACKGROUND

NMR studies of denatured states, both fully unfolded and partially folded, give insight into the conformations and interactions formed during folding. Although the complete structural characterization of partially folded proteins is a very difficult task, the identification of structured subsets, such as hydrophobic clusters, is of value in understanding the structural organization of such states. Here, we report the NMR characterization, in acidic conditions (pH 2), of a well-defined hydrophobic cluster localized in the core of bovine beta-lactoglobulin.

RESULTS

The existence of a small hydrophobic cluster present in the lipocalin protein family has been assessed on the basis of structural alignment and NRM data obtained for the partially folded bovine beta-lactoglobulin. The presence of the cluster had been predicted identifying those residues that are highly conserved in most members of the family. An NMR study conducted at pH 2, where the protein exhibits a very stable beta-core together with disordered regions, reveals the presence of NOEs among sidechains of 11 hydrophobic residues centered around Trp19 and pointing towards the interior of the protein. This buried cluster is found to be unusually stable at pH 2, not only at room temperature but also at 323K. Furthermore, conserved hydrophobic residues pointing towards the surface of the protein define a hydrophobic surface patch located in a groove between the strands and the helix.

CONCLUSIONS

The detected buried cluster most likely plays an important role in bovine beta-lactoglobulin stability. The analysis of five structurally related proteins reveals that the same extended cluster is present in these structures. We propose that the buried cluster may represent the internal binding site as well and that the hydrophobic surface patch is involved in a second external binding site.

Effects of pH and salt environment on the association of beta-lactoglobulin revealed by intrinsic fluorescence studies

The effects of pH, ionic strength and heat on the structure of beta-lactoglobulin (beta-lg) have been investigated by studying the intrinsic tryptophan fluorescence of the protein. Between pH 2 and 9, for sodium chloride concentrations varying from 0.0 to 0.2 M, the position of the fluorescence emission maximum at 20 degrees C remained constant at 328 nm, suggesting that the hydrophobic environment of the fluorophores remained unchanged. The fluorescence intensity increased significantly at pH 2, 7 and 9 on reducing the NaCl concentration of the solutions. The most likely explanation for this, supported by recent light scattering data, is that the presence of NaCl is necessary for beta-lg to dimerize. At the higher NaCl concentrations it was found that dimerization accompanied a reduction in fluorescence intensity. Thus, dissociation appears to reduce the self-quenching of tryptophan residues that occurs within the dimer. The fluorescence of solutions heated below the denaturation temperature reflected the state of association of the protein molecules. Above the denaturation temperature and associated with protein aggregation, an irreversible increase in intrinsic tryptophan fluorescence was observed. We also report what we believe to be the first front-face fluorescence measurements on globular protein gels, showing effects of pH and NaCl concentration.

Bovine beta-lactoglobulin at 1.8 A resolution--still an enigmatic lipocalin

BACKGROUND

beta-Lactoglobulin (beta-Lg) is the major whey protein in the milk of ruminants and many other mammals. Its function is not known, but it undergoes at least two pH-dependent conformational changes which may be important. Bovine beta-Lg crystallizes in several different lattices, and medium-resolution structures of orthorhombic lattice Y and trigonal lattice Z have been published. Triclinic lattice X and lattice Z crystals grow at pH values either side of the pH at which one of the pH-induced conformational changes occurs. A full understanding of the structure is needed to help explain both the conformational changes and the different denaturation behaviour of the genetic variants.

RESULTS

We have redetermined the structure of beta-Lg lattice Z at 3.0 A resolution by multiple isomorphous replacement and have partially refined it (R factor = 24.8%). Using the dimer from this lattice Z structure as a search model, the triclinic crystal form grown at pH 6.5 (lattice X) has been solved by molecular replacement. Refinement of lattice X at 1.8 A resolution gave an R factor of 18.1%. The structure we have determined differs from previously published structures in several ways.

CONCLUSIONS

Incorrect threading of the sequence in the published structures of beta-Lg affects four of the nine beta strands. The basic lipocalin fold of the polypeptide chain is unchanged, however. The relative orientation of the monomers in the beta-Lg dimer differs in the two lattices. On raising the pH, there is a rotation of approximately 5 degrees, which breaks a number of intersubunit hydrogen bonds. It is not yet clear, however, why the stability of the structure should depend so heavily upon the external loop around residue 64 or the beta strand with the free thiol, each of which shows genetic variation.

Molten globule state of equine beta-lactoglobulin

The acid-unfolded state of equine beta-lactoglobulin was characterized by means of circular dichroism, nuclear magnetic resonance, analytical gel-filtration chromatography, and analytical centrifugation. The acid-unfolded state of equine beta-lactoglobulin has a substantial secondary structure as shown by the far-ultraviolet circular dichroism spectrum but lacks persistent tertiary packing of the side chains as indicated by the near-ultraviolet circular dichroism and nuclear magnetic resonance spectra. It is nearly as compact as the native conformation as shown by the gel filtration and sedimentation experiments, and it has the exposed hydrophobic surface as indicated by its tendency to aggregate. All of these characteristics indicate that the acid-unfolded state of equine beta-lactoglobulin is a molten globule state. The alpha helix content in the acid-unfolded state, which has been estimated from the circular dichroism spectrum, is larger than that in the native state, suggesting the presence of nonnative alpha helices in the molten globule state. This result suggests the generality of the intermediate with nonnative alpha helices during the folding of proteins having the beta-clam fold.

Antigen-specific inhibition of CD4+ T-cell responses to beta-lactoglobulin by its single amino acid-substituted mutant form through T-cell receptor antagonism

T-cell responses can be antagonized by some single amino acid-substituted analogs of a peptide ligand for T-cell receptors (TCR), and these are called TCR antagonists. In this study, we addressed the question of whether TCR antagonism can be elicited by a whole protein antigen carrying a mutated T-cell determinant region corresponding to a TCR antagonist peptide. To clarify this, we examined the ability of a single amino acid-substituted mutant form of bovine beta-lactoglobulin (beta-Lg) to inhibit three CD4+ T-cell clones recognizing a peptide corresponding to an immunodominant determinant region 119-133 of beta-Lg (p119-133). First, we identified pD129A, an analog of p119-133 with a substitution of Ala for 129Asp, as an antagonist which can inhibit the response of two of the three T-cell clones. Then, using a yeast expression system, we prepared a mutant beta-Lg (mutD129A) with the same substitution of Ala for 129Asp as that in pD129A. This mutant protein could inhibit the proliferation of the two T-cell clones in a manner similar to the effect of pD129A. From these results we can demonstrate that TCR antagonism can be elicited by peptides naturally processed from a single-substituted mutant protein as well as by the corresponding peptides added exogenously.

Fine mapping of T-cell determinants of bovine beta-lactoglobulin

T-cell recognition sites, i.e. T-cell determinants, of bovine beta-lactoglobulin, a major allergen in milk, were analyzed in detail. For this purpose, we prepared primary cultures of lymph node cells from three strains of mice, C57BL/6 (H-2b), C3H/HeN (H-2k), and BALB/c (H-2d), and examined the proliferative response of these cells to a complete set of overlapping 15-mer peptides which covered the entire sequence of beta-lactoglobulin by shifting in single amino acid steps. We were able to determine the putative core sequence of each T-cell determinant and estimate its relative importance. In the case of C57BL/6 mice, dominant, subdominant, and minor determinants were identified as residues 122-130, 16-26, and 108-122, respectively, as represented by their core sequences. Each determinant peptide induced the production of interferon-gamma, the amount of which showed a correlation with the intensity of the proliferative response induced by each determinant. In the case of C3H/HeN mice, a dominant determinant comprised of residues 140-148 was identified together with three subdominant and two minor determinants. Dominant T-cell determinants recognized in BALB/c mice were identified as residues 67-75, 71-79, and 80-88, and six other regions were identified as subdominant determinants. Comparisons between our results and the determinants predicted from relevant MHC-binding motifs reported to date revealed the inadequacy of the motifs in predicting even the dominant determinants. The information obtained by complete mapping of T-cell determinants as done in this study is expected to be helpful in establishment and evaluation of new prediction methods and also may contribute to the development of a new approach to control immune responses by manipulation of the T-cell determinants of allergens.

In vitro renaturation of bovine beta-lactoglobulin A leads to a biologically active but incompletely refolded state

When bovine beta-lactoglobulin (beta-LG) was refolded after extensive denaturation in 4.8 M guanidine hydrochloride (GuHCl), the functional activity of the protein, retinol binding, as measured by the enhancement of this ligand's fluorescence, was completely recovered. In contrast, the room-temperature tryptophan phosphorescence lifetime of the refolded protein, a local measure of the residue environment, was approximately 10 ms, significantly shorter than the phosphorescence lifetime of the untreated native protein (approximately 20 ms). The lability of the freshly refolded protein, as monitored by following the time course of its unfolding when incubated in 2.5 M GuHCl through the change in fluorescence intensity at 385 nm, was also determined and found to be increased significantly relative to untreated native protein. In contrast to the long term postactivation conformational changes detected previously in Escherichia coli alkaline phosphatase (Subramaniam V, Bergenhem NCH, Gafni A, Steel DG, 1995, Biochemistry 34:1133-1136), we found no changes in either the lability or phosphorescence decays of beta-LG during a period of 24 h. Our results are in agreement with the report by Hattori et al. (1993, J Biol Chem 268:22414-22419), using conformation-specific monoclonal antibodies to recognize native-like structure, that long-term changes occur in the protein conformation, compared with the native structure, on refolding.

Expression and secretion of recombinant ovine beta-lactoglobulin in Saccharomyces cerevisiae and Kluyveromyces lactis

High expression and secretion of recombinant ovine beta-lactoglobulin has been achieved in the yeast Kluyveromyces lactis. The yield of beta-lactoglobulin is 40-50 mg per litre of culture supernatant and accounts for approx. 72% of the total secreted protein. Constitutive expression is under the control of the Saccharomyces cerevisiae phosphoglycerate kinase promoter from an intronless version of the beta-lactoglobulin gene. Secretion is specified by the ovine protein's own signal sequence. this system, coupled to an efficient and novel recovery protocol, allows 30 mg of pure protein to be isolated from a typical 1 litre culture. The protein is virtually indistinguishable from beta-lactoglobulin conventionally purified from sheep milk by its behaviour in native PAGE and SDS/PAGE, reactivity to antibodies, CD, fluorescence spectroscopy and N-terminal sequencing. Attempts to achieve a similar expression and secretion system in the yeast S. cerevisiae met with only limited success, although it was found that heat-shock treatment modestly increased the yield up to approx. 3-4 mg per litre of culture supernatant. Site-directed mutagenesis showed that secretion in S. cerevisiae depended upon correct formation of the two disulphide bonds present in beta-lactoglobulin.

Cloning and expression of human neutrophil lipocalin cDNA derived from bone marrow and ovarian cancer cells

Human neutrophil lipocalin (HNL) cDNA was amplified by PCR technology in combination with deoxyinosine containing oligonucleotides for cloning, sequencing and production of the recombinant protein in E. coli. The primers were targeted to the corresponding DNA backtranslate of the mature protein resulting in a PCR amplified 534 bp cDNA from different reverse transcripts of ovarian cancer cell line and bone marrow cell mRNAs. Sequence analysis revealed that two different cDNAs from ovarian cancer and bone marrow cells could be obtained. Cloning and expression of HNL cDNAs were performed in E. coli strain HMS 174 [DE3] using the pET system yielding in two recombinant proteins with a molecular weight of 21 kDa which is consistent with an 178 amino acid residues containing sequence of the mature HNL protein. N-terminal amino acid sequence analysis of the expression products showed an identical polypeptide sequence missing the E. coli processed starting methionine.