Apo-parvalbumin as an intrinsically disordered protein

Comparative studies of seafood and reptile α- and β-parvalbumins

Small calcium-binding proteins such as parvalbumins (PVs) are major seafood and fish allergens. However, the impact of structural changes on their capacity to bind IgE has not been studied in detail. Therefore, fish and reptilian PVs, as well as human α-PV, were selected for biochemical, structural, and IgE binding studies. Likely due to their high solubility, crystallization proved difficult, so additional techniques were used to promote crystallization of the proteins. Novel crystal structures were determined for human PV, cod allergen Gad m 1.0201, saltwater crocodile allergen Cro p 1.0101, and the α-PV from thornback ray. β-PVs are considered the major fish allergens, while α-PVs are rarely categorized as allergens. To explain these differences, the results of structural and IgE binding studies were combined. This approach allowed us to provide new insight into IgE binding epitopes present on PVs, focusing on cross-reactivity among the selected α- and β-PVs. In addition, we have shown that these proteins display remarkable thermal stability across a range of pH conditions, which is relevant in the case of food allergens and food processing. Moreover, it is shown that the presence of calcium cations is critical for stability of the studied PVs via their protein folding, which has an impact on the formation of IgE binding epitopes. These studies shows the stability of fish and reptile PV allergens, and it allows for further evaluation of their IgE cross-reactivity.

Detection of Parvalbumin Fish Allergen in Canned Tuna by Real-Time PCR Driven by Tuna Species and Can-Filling Medium

Canned tuna is considered one of the most popular and most commonly consumed products in the seafood market, globally. However, in past decades, fish allergens have been detected as the main concern regarding food safety in these seafood products and are listed as the top eight food allergies. In the group of fish allergens, parvalbumin is the most common. As a thermally stable and calcium-binding protein, parvalbumin can be easily altered with changing the food matrices. This study investigated the effect of a can-filling medium (tomato sauce, spices, and brine solutions) on the parvalbumin levels in canned tuna. The effect of pH, calcium content, and the DNA quality of canned tuna was also investigated before the parvalbumin-specific encoded gene amplification. The presence of fish allergens was determined by melting curve analyses and confirmed by agarose gel electrophoresis. The obtained results showed that the presence of parvalbumin in commercially canned tuna was driven by can-filling mediums, thermal conductivity, calcium content, and the acidity of various ingredients in food matrices. The intra-specific differences revealed a variation in fish allergens that are caused by cryptic species. This study proved that allergens encoding gene analyses by agarose electrophoresis could be used as a reliable approach for other food-borne allergens in complex food matrices.

Fish Allergenicity Modulation Using Tailored Enriched Diets—Where Are We?

Food allergy is an abnormal immune response to specific proteins in a certain food. The chronicity, prevalence, and the potential fatality of food allergy, make it a serious socio-economic problem. Fish is considered the third most allergenic food in the world, affecting part of the world population with a higher incidence in children and adolescents. The main allergen in fish, responsible for the large majority of fish-allergic reactions in sensitized patients, is a small and stable calcium-binding muscle protein named beta-parvalbumin. Targeting the expression or/and the 3D conformation of this protein by adding specific molecules to fish diets has been the innovative strategy of some researchers in the fields of fish allergies and nutrition. This has shown promising results, namely when the apo-form of β-parvalbumin is induced, leading in the case of gilthead seabream to a 50% reduction of IgE-reactivity in fish allergic patients.

What Is Parvalbumin for?

Parvalbumin (PA) is a small, acidic, mostly cytosolic Ca2+-binding protein of the EF-hand superfamily. Structural and physical properties of PA are well studied but recently two highly conserved structural motifs consisting of three amino acids each (clusters I and II), which contribute to the hydrophobic core of the EF-hand domains, have been revealed. Despite several decades of studies, physiological functions of PA are still poorly known. Since no target proteins have been revealed for PA so far, it is believed that PA acts as a slow calcium buffer. Numerous experiments on various muscle systems have shown that PA accelerates the relaxation of fast skeletal muscles. It has been found that oxidation of PA by reactive oxygen species (ROS) is conformation-dependent and one more physiological function of PA in fast muscles could be a protection of these cells from ROS. PA is thought to regulate calcium-dependent metabolic and electric processes within the population of gamma-aminobutyric acid (GABA) neurons. Genetic elimination of PA results in changes in GABAergic synaptic transmission. Mammalian oncomodulin (OM), the β isoform of PA, is expressed mostly in cochlear outer hair cells and in vestibular hair cells. OM knockout mice lose their hearing after 3–4 months. It was suggested that, in sensory cells, OM maintains auditory function, most likely affecting outer hair cells’ motility mechanisms.

Strontium Binding to α-Parvalbumin, a Canonical Calcium-Binding Protein of the "EF-Hand" Family

Strontium salts are used for treatment of osteoporosis and bone cancer, but their impact on calcium-mediated physiological processes remains obscure. To explore Sr²⁺ interference with Ca²⁺ binding to proteins of the EF-hand family, we studied Sr²⁺/Ca²⁺ interaction with a canonical EF-hand protein, α-parvalbumin (α-PA). Evaluation of the equilibrium metal association constants for the active Ca²⁺ binding sites of recombinant human α-PA (‘CD’ and ‘EF’ sites) from fluorimetric titration experiments and isothermal titration calorimetry data gave 4 × 10⁹ M⁻¹ and 4 × 10⁹ M⁻¹ for Ca²⁺, and 2 × 10⁷ M⁻¹ and 2 × 10⁶ M⁻¹ for Sr²⁺. Inactivation of the EF site by homologous substitution of the Ca²⁺-coordinating Glu in position 12 of the EF-loop by Gln decreased Ca²⁺/Sr²⁺ affinity of the protein by an order of magnitude, whereas the analogous inactivation of the CD site induced much deeper suppression of the Ca²⁺/Sr²⁺ affinity. These results suggest that Sr²⁺ and Ca²⁺ bind to CD/EF sites of α-PA and the Ca²⁺/Sr²⁺ binding are sequential processes with the CD site being occupied first. Spectrofluorimetric Sr²⁺ titration of the Ca²⁺-loaded α-PA revealed presence of secondary Sr²⁺ binding site(s) with an apparent equilibrium association constant of 4 × 10⁵ M⁻¹. Fourier-transform infrared spectroscopy data evidence that Ca²⁺/Sr²⁺-loaded forms of α-PA exhibit similar states of their COO⁻ groups. Near-UV circular dichroism (CD) data show that Ca²⁺/Sr²⁺ binding to α-PA induce similar changes in symmetry of microenvironment of its Phe residues. Far-UV CD experiments reveal that Ca²⁺/Sr²⁺ binding are accompanied by nearly identical changes in secondary structure of α-PA. Meanwhile, scanning calorimetry measurements show markedly lower Sr²⁺-induced increase in stability of tertiary structure of α-PA, compared to the Ca²⁺-induced effect. Theoretical modeling using Density Functional Theory computations with Polarizable Continuum Model calculations confirms that Ca²⁺-binding sites of α-PA are well protected against exchange of Ca²⁺ for Sr²⁺ regardless of coordination number of Sr²⁺, solvent exposure or rigidity of sites. The latter appears to be a key determinant of the Ca²⁺/Sr²⁺ selectivity. Overall, despite lowered affinity of α-PA to Sr²⁺, the latter competes with Ca²⁺ for the same EF-hands and induces similar structural rearrangements. The presence of a secondary Sr²⁺ binding site(s) could be a factor contributing to Sr²⁺ impact on the functional activity of proteins.

Effect of EDTA enriched diets on farmed fish allergenicity and muscle quality; a proteomics approach

Fish is one of the most common elicitors of food-allergic reactions worldwide. These reactions are triggered by the calcium-binding muscle protein β-parvalbumin, which was shown to have reduced immunoglobulin E (IgE)-binding capacity upon calcium depletion. This work aimed to reduce gilthead seabream allergenicity using diets supplemented with a calcium chelator. Three experimental feeds were tested, differing in ethylenediaminetetraacetic acid (EDTA) supplementation, and its effects on muscle and parvalbumin's IgE-reactivity were analyzed. Chromatographic determination of EDTA showed no accumulation in the muscle and sensory results demonstrated that the lowest concentration did not affect fish quality as edible fish. Proteomics revealed one protein related to muscle contraction with significantly different relative abundance. Immunoblot assays performed with fish-allergic patients sera indicated a 50% reduction in IgE-reactivity upon EDTA presence. These preliminary results provide the basis for the further development of a non-GMO approach to modulate fish allergenicity and improve safety of aquaculture fish.

Analyzing the structural and functional roles of residues from the 'black' and 'gray' clusters of human S100P protein

Two highly conserved structural motifs observed in members of the EF-hand family of calcium binding proteins. The motifs provide a supporting scaffold for the Ca2+ binding loops and contribute to the hydrophobic core of the EF-hand domain. Each structural motif represents a cluster of three amino acids called cluster I ('black' cluster) and cluster II ('grey' cluster). Cluster I is more conserved and mostly incorporates aromatic amino acids. In contrast, cluster II is noticeably less conserved and includes a mix of aromatic, hydrophobic, and polar amino acids of different sizes. In the human calcium binding S100 P protein, these 'black' and 'gray' clusters include residues F15, F71, and F74 and L33, L58, and K30, respectively. To evaluate the effects of these clusters on structure and functionality of human S100 P, we have performed Ala scanning. The resulting mutants were studied by a multiparametric approach that included circular dichroism, scanning calorimetry, dynamic light scattering, chemical crosslinking, and fluorescent probes. Spectrofluorimetric Ca2+-titration of wild type S100 P showed that S100 P dimer has 1-2 strong calcium binding sites (K₁ = 4 × 106 M^-1) and two cooperative low affinity (K₂ = 4 × 104 M^-1) binding sites. Similarly, the S100 P mutants possess two types of calcium binding sites. This analysis revealed that the alanine substitutions in the clusters I and II caused comparable changes in the S100 P functional properties. However, analysis of heat- or GuHCl-induced unfolding of these proteins showed that the alanine substitutions in the cluster I caused notably more pronounced decrease in the protein stability compared to the changes caused by alanine substitutions in the cluster II. Opposite to literature data, the F15 A substitution did not cause the S100 P dimer dissociation, indicating that F15 is not crucial for dimer stability. Overall, similar to parvalbumins, the S100 P cluster I is more important for protein conformational stability than the cluster II.

The yeast GRASP Grh1 displays a high polypeptide backbone mobility along with an amyloidogenic behavior

GRASPs are proteins involved in cell processes that seem paradoxical: responsible for shaping the Golgi cisternae and involved in unconventional secretion mechanisms that bypass the Golgi. Despite its physiological relevance, there is still a considerable lack of studies on full-length GRASPs. Our group has previously reported an unexpected behavior of the full-length GRASP from the fungus C. neoformans: its intrinsically-disordered characteristic. Here, we generalize this finding by showing that it is also observed in the GRASP from S. cerevisae (Grh1), which strongly suggests it might be a general property within the GRASP family. Furthermore, Grh1 is also able to form amyloid-like fibrils either upon heating or when submitted to changes in the dielectric constant of its surroundings, a condition that is experienced by the protein when in close contact with membranes of cell compartments, such as the Golgi apparatus. Intrinsic disorder and fibril formation can thus be two structural properties exploited by GRASP during its functional cycle.

Small Angle Neutron Scattering Studies of R67 Dihydrofolate Reductase, a Tetrameric Protein with Intrinsically Disordered N-Termini

R67 dihydrofolate reductase (DHFR) is a homotetramer with a single active site pore and no sequence or structural homology with chromosomal DHFRs. The R67 enzyme provides resistance to trimethoprim, an active site-directed inhibitor of Escherichia coli DHFR. Sixteen to twenty N-terminal amino acids are intrinsically disordered in the R67 dimer crystal structure. Chymotrypsin cleavage of 16 N-terminal residues results in an active enzyme with a decreased stability. The space sampled by the disordered N-termini of R67 DHFR was investigated using small angle neutron scattering. From a combined analysis using molecular dynamics and the program SASSIE ( http://www.smallangles.net/sassie/SASSIE_HOME.html ), the apoenzyme displays a radius of gyration (Rg) of 21.46 ± 0.50 Å. Addition of glycine betaine, an osmolyte, does not result in folding of the termini as the Rg increases slightly to 22.78 ± 0.87 Å. SASSIE fits of the latter SANS data indicate that the disordered N-termini sample larger regions of space and remain disordered, suggesting they might function as entropic bristles. Pressure perturbation calorimetry also indicated that the volume of R67 DHFR increases upon addition of 10% betaine and decreased at 20% betaine because of the dehydration of the protein. Studies of the hydration of full-length R67 DHFR in the presence of the osmolytes betaine and dimethyl sulfoxide find around 1250 water molecules hydrating the protein. Similar studies with truncated R67 DHFR yield around 400 water molecules hydrating the protein in the presence of betaine. The difference of ∼900 waters indicates the N-termini are well-hydrated.

Tyrosine fluorescence probing of conformational changes in tryptophan-lacking domain of albumins

We addressed the possibility of using tyrosine (Tyr) fluorescence for monitoring conformational changes of proteins which are undetectable via tryptophan (Trp) fluorescence. The model objects, human (HSA) and bovine (BSA) serum albumins, contain one and two Trp residues, respectively, while Tyr is more uniformly distributed over their structure. The results of the investigation of albumins interaction with ethanol using intrinsic Trp and Tyr steady-state and time-resolved picosecond fluorescence indicated the presence of an intermediate at 10% (v/v) of ethanol in solution, that was supported by the results of extrinsic fluorescence measurements with the Nile Red dye. Based on the comparison of HSA and BSA Trp and Tyr fluorescence, it was suggested that conformational changes at low ethanol concentration are located in the domain III of albumins, which lacks tryptophan residues. The sensitivity of Tyr fluorescence to domain III alterations was further verified by studying albumins interaction with GdnHCl.

Calcium Binding and Disulfide Bonds Regulate the Stability of Secretagogin towards Thermal and Urea Denaturation

Secretagogin is a calcium-sensor protein with six EF-hands. It is widely expressed in neurons and neuro-endocrine cells of a broad range of vertebrates including mammals, fishes and amphibia. The protein plays a role in secretion and interacts with several vesicle-associated proteins. In this work, we have studied the contribution of calcium binding and disulfide-bond formation to the stability of the secretagogin structure towards thermal and urea denaturation. SDS-PAGE analysis of secretagogin in reducing and non-reducing conditions identified a tendency of the protein to form dimers in a redox-dependent manner. The denaturation of apo and Calcium-loaded secretagogin was studied by circular dichroism and fluorescence spectroscopy under conditions favoring monomer or dimer or a 1:1 monomer: dimer ratio. This analysis reveals significantly higher stability towards urea denaturation of Calcium-loaded secretagogin compared to the apo protein. The secondary and tertiary structure of the Calcium-loaded form is not completely denatured in the presence of 10 M urea. Reduced and Calcium-loaded secretagogin is found to refold reversibly after heating to 95°C, while both oxidized and reduced apo secretagogin is irreversibly denatured at this temperature. Thus, calcium binding greatly stabilizes the structure of secretagogin towards chemical and heat denaturation.

Extremophilic 50S Ribosomal RNA-Binding Protein L35Ae as a Basis for Engineering of an Alternative Protein Scaffold

Due to their remarkably high structural stability, proteins from extremophiles are particularly useful in numerous biological applications. Their utility as alternative protein scaffolds could be especially valuable in small antibody mimetic engineering. These artificial binding proteins occupy a specific niche between antibodies and low molecular weight substances, paving the way for development of innovative approaches in therapeutics, diagnostics, and reagent use. Here, the 50S ribosomal RNA-binding protein L35Ae from the extremophilic archaea Pyrococcus horikoshii has been probed for its potential to serve as a backbone in alternative scaffold engineering. The recombinant wild type L35Ae has a native-like secondary structure, extreme thermal stability (mid-transition temperature of 90°C) and a moderate resistance to the denaturation by guanidine hydrochloride (half-transition at 2.6 M). Chemical crosslinking and dynamic light scattering data revealed that the wild type L35Ae protein has a propensity for multimerization and aggregation correlating with its non-specific binding to a model cell surface of HEK293 cells, as evidenced by flow cytometry. To suppress these negative features, a 10-amino acid mutant (called L35Ae 10X) was designed, which lacks the interaction with HEK293 cells, is less susceptible to aggregation, and maintains native-like secondary structure and thermal stability. However, L35Ae 10X also shows lowered resistance to guanidine hydrochloride (half-transition at 2.0M) and is more prone to oligomerization. This investigation of an extremophile protein’s scaffolding potential demonstrates that lowered resistance to charged chemical denaturants and increased propensity to multimerization may limit the utility of extremophile proteins as alternative scaffolds.

Two structural motifs within canonical EF-hand calcium-binding domains identify five different classes of calcium buffers and sensors

Proteins with EF-hand calcium-binding motifs are essential for many cellular processes, but are also associated with cancer, autism, cardiac arrhythmias, and Alzheimer's, skeletal muscle and neuronal diseases. Functionally, all EF-hand proteins are divided into two groups: (1) calcium sensors, which function to translate the signal to various responses; and (2) calcium buffers, which control the level of free Ca²⁺ ions in the cytoplasm. The borderline between the two groups is not clear, and many proteins cannot be described as definitive buffers or sensors. Here, we describe two highly-conserved structural motifs found in all known different families of the EF-hand proteins. The two motifs provide a supporting scaffold for the DxDxDG calcium binding loop and contribute to the hydrophobic core of the EF hand domain. The motifs allow more precise identification of calcium buffers and calcium sensors. Based on the characteristics of the two motifs, we could classify individual EF-hand domains into five groups: (1) Open static; (2) Closed static; (3) Local dynamic; (4) Dynamic; and (5) Local static EF-hand domains.

Fish allergens at a glance: variable allergenicity of parvalbumins, the major fish allergens

Fish is a common trigger of severe, food-allergic reactions. Only a limited number of proteins induce specific IgE-mediated immune reactions. The major fish allergens are the parvalbumins. They are members of the calcium-binding EF-hand protein family characterized by a conserved protein structure. They represent highly cross-reactive allergens for patients with specific IgE to conserved epitopes. These patients might experience clinical reactions with various fish species. On the other hand, some individuals have IgE antibodies directed against unique, species-specific parvalbumin epitopes, and these patients show clinical symptoms only with certain fish species. Furthermore, different parvalbumin isoforms and isoallergens are present in the same fish and might display variable allergenicity. This was shown for salmon homologs, where only a single parvalbumin (beta-1) isoform was identified as allergen in specific patients. In addition to the parvalbumins, several other fish proteins, enolases, aldolases, and fish gelatin, seem to be important allergens. New clinical and molecular insights advanced the knowledge and understanding of fish allergy in the last years. These findings were useful for the advancement of the IgE-based diagnosis and also for the management of fish allergies consisting of advice and treatment of fish-allergic patients.

Structural characterization of more potent alternatives to HAMLET, a tumoricidal complex of α-lactalbumin and oleic acid

HAMLET is a complex of human α-lactalbumin (hLA) with oleic acid (OA) that kills various tumor cells and strains of Streptococcus pneumoniae. More potent protein-OA complexes were previously reported for bovine α-lactalbumin (bLA) and β-lactoglobulin (bLG), and pike parvalbumin (pPA), and here we explore their structural features. The concentration dependencies of the tryptophan fluorescence of hLA, bLA, and bLG complexes with OA reveal their disintegration at protein concentrations below the micromolar level. Chemical cross-linking experiments provide evidence that association with OA shifts the distribution of oligomeric forms of hLA, bLA, bLG, and pPA toward higher-order oligomers. This effect is confirmed for bLA and bLG using the dynamic light scattering method, while pPA is shown to associate with OA vesicles. Like hLA binding, OA binding increases the affinity of bLG for small unilamellar dipalmitoylphosphatidylcholine vesicles, while pPA efficiently binds to the vesicles irrespective of OA binding. The association of OA with bLG and pPA increases their α-helix and cross-β-sheet content and resistance to enzymatic proteolysis, which is indicative of OA-induced protein structuring. The lack of excess heat sorption during melting of bLG and pPA in complex with OA and the presence of a cooperative thermal transition at the level of their secondary structure suggest that the OA-bound forms of bLG and pPA lack a fixed tertiary structure but exhibit a continuous thermal transition. Overall, despite marked differences, the HAMLET-like complexes that were studied exhibit a common feature: a tendency toward protein oligomerization. Because OA-induced oligomerization has been reported for other proteins, this phenomenon is inherent to many proteins.

Sequence microheterogeneity of parvalbumin, the major fish allergen

The microheterogeneity of amino acid sequence observed in various allergens may affect immune response, but incidence of sequence microheterogeneity in allergens and its relation to their allergenicity are unclear. The occurrence of sequence microheterogeneity in major fish allergen, parvalbumin (PA), has been explored using bioinformatics approaches. 44% of 111 species with known PA sequence have PA isoforms. 41% of these species exhibit from 1 to 4 cases of PA sequence microheterogeneity, i.e. unique pairs of PA isoforms with sequence identity above 90%. 29% of 210 PA sequences studied are characterized by microheterogeneity. The occurrence of allergens among them is 2.5-fold higher than among other PAs. The incidence of sequence microheterogeneity within more allergenic β isoform of PA is 2.0-fold lower than that for its less allergenic α isoform. 39 residues affected by PA microheterogeneity are concentrated in the region of helices A, B, F, while helices D and E are the most conservative region. 44% and 11% of the microheterogeneous substitutions are located in the species-specific and cross-reactive IgE-binding epitopes of PAs, respectively. 45% and 48% of the substitution cases are predicted to cause notable changes in protein disorder propensity and protein stability, respectively. Hence, the increased allergenicity rate among PAs having microheterogeneous isoforms can be related to differences in their IgE-binding caused directly or in an allosteric manner. Overall, sequence microheterogeneity is shown to be inherent to many of PAs and likely contributes to PA allergenicity.

Metal-specific structural changes in parvalbumin

Parvalbumin is a small protein of EF-hand family whose main role is considered to be metal buffering. Recent evidences indicate that parvalbumin also fulfills more complicated functions, which may be determined by the diversity in structural changes in response to the binding of different metal cations. In the present work the conformations of α and β isoforms of pike parvalbumin in the Ca(2+)- and Mg(2+)-loaded state were studied by intrinsic fluorescence, circular dichroism and bis-ANS extrinsic fluorescence. We have determined the structural region causing different spectral response on the binding of Mg(2+)- and Ca(2+) ions in pike β-parvalbumin. Our data reveal similarity of the metal-bound forms of α-parvalbumin. In contrast, those of β isoform differ significantly in the tyrosine spectral range. We also discuss the possible physiological consequences of the structural rearrangements accompanied Mg(2+)/Ca(2+) exchange in pike β-parvalbumin.

Hydrophobic moments, shape, and packing in disordered proteins

Disordered proteins play a significant role in many biological processes and provide an attractive target for biophysical studies under physiological conditions. Disordered proteins may be classified as (a) proteins with overall well-defined secondary structures, interspersed with regions of missing residues, or (b) natively unstructured proteins which lack definite secondary structure. The spatial profile of second order hydrophobic moment for disordered proteins depicts the distribution of hydrophobic residues from the interior to the surface of the protein and indicates the lack of a well-formed hydrophobic core unlike that of the globular proteins. This trend is independent of the size or position of the disordered region in the sequence. The hydrophobicity profile of the ordered regions of the disordered proteins differ considerably from that of globular proteins implying the role of disordered parts and the significance of hydrophobic interactions in the folding of proteins. The shape asymmetry of the two classes of disordered proteins is determined by calculating the asphercity and shape parameters, derived from the cartesian components of radius of gyration tensor. Disordered proteins of group a are more spherical as compared to the natively unstructured proteins (group b), which are more prolate. Both groups of proteins exhibit similar types of side-chain backbone contacts, as that of the globular proteins. While disordered proteins contains few hydrophobic residues natively unstructured proteins are characterized by a residues of low mean hydrophobicity and high mean net charge.

The effect of counter ions on the conformation of intrinsically disordered proteins studied by size-exclusion chromatography

Counter ions are able to change the conformation of intrinsically disordered proteins (IDPs) to a more compact structure via the reduction of electrostatic repulsion. When the extended IDP conformation is transformed into a more ordered one, the value of the Stokes radius should decrease. Size-exclusion chromatography is a simple method for the determination of the Stokes radius, which describes the hydrodynamic properties of protein molecules. In our paper size-exclusion chromatography experiments of Starmaker (a highly acidic IDP), in the presence of various counter ions, are presented as an example of a simple experimental method, which provides valuable information about subtle counter ions-induced conformational changes in IDP.

Differential scanning microcalorimetry of intrinsically disordered proteins

Ultrasensitive differential scanning calorimetry (DSC) is an indispensable thermophysical technique enabling to get direct information on enthalpies accompanying heating/cooling of dilute biopolymer solutions. The thermal dependence of protein heat capacity extracted from DSC data is a valuable source of information on intrinsic disorder level of a protein. Application details and limitations of DSC technique in exploration of protein intrinsic disorder are described.

The use of UV-Vis absorption spectroscopy for studies of natively disordered proteins

Absorption spectroscopy can be used to monitor structural changes upon transitions from ordered to disordered state in proteins. Changes in environment of tryptophan, tyrosine, and phenylalanine residues result in changes of their absorption spectra. In most cases the changes are small and can be measured only in a differential mode.

Temperature and solvent dependence of the dynamical landscape of tau protein conformations

We report the variation with temperature of the ensemble distribution of conformations spanned by the tau protein in its dynamical states measured by small-angle X-ray scattering (SAXS) using synchrotron radiation. The SAXS data show a clear temperature variation of the distribution of occupied protein conformations from 293 to 318 K. More conformations with a smaller radius of gyration are occupied at higher temperature. The protein-solvent interactions are shown by computer simulation to be essential for controlling the dynamics of protein conformations, providing evidence for the key role of water solvent in the protein dynamics, as proposed by Giorgio Careri.

Evaluation and comparison of the species-specificity of 3 antiparvalbumin IgG antibodies

Parvalbumin is a pan-allergen in fish and frogs that triggers IgE-mediated reactions in fish-allergic individuals. Previous studies demonstrated that antibodies raised against fish and frog parvalbumins displayed varying specificity for different fish species, and thus, the applicability of these antibodies for potential use in immunoassays to detect fish residues were limited. We aimed to determine the specificity of 3 IgG antibodies for various fish species. Indirect enzyme-linked immunosorbent assay (ELISA) and IgG-immunoblotting were used to compare the reactivity of the polyclonal anticod parvalbumin antibody and the commercially available, monoclonal antifrog and monoclonal anticarp parvalbumin antibodies against raw muscle extracts of 29 fish species. All antibodies demonstrated varying specificities for different fish species. Of the 3 antibodies, the polyclonal anticod parvalbumin antibody is the most suitable for the detection of fish parvalbumins as it showed reactivity to the widest range of species, including herring, pilchard, carp, pike, cod, pollock, haddock, cusk, hake, bluegill, tilapia, bass, grouper, trout, catfish, and perch, although detection was still limited for several key fish species.

Energy landscape analyses of disordered histone tails reveal special organization of their conformational dynamics

Histone tails are highly flexible N- or C-terminal protrusions of histone proteins which facilitate the compaction of DNA into dense superstructures known as chromatin. On a molecular scale histone tails are polyelectrolytes with high degree of conformational disorder which allows them to function as biomolecular "switches", regulating various genetic processes. Unfortunately, their intrinsically disordered nature creates obstacles for comprehensive experimental investigation of both the structural and dynamical aspects of histone tails, because of which their conformational behaviors are still not well understood. In this work we have carried out ∼3 microsecond long all atom replica exchange molecular dynamics (REMD) simulations for each of four histone tails, H4, H3, H2B, and H2A, and probed their intrinsic conformational preferences. Our subsequent free energy landscape analysis demonstrated that most tails are not fully disordered, but show distinct conformational organization, containing specific flickering secondary structural elements. In particular, H4 forms β-hairpins, H3 and H2B adopt α-helical elements, while H2A is fully disordered. We rationalized observed patterns of conformational dynamics of various histone tails using ideas from physics of polyelectrolytes and disordered systems. We also discovered an intriguing re-entrant contraction-expansion of the tails upon heating, which is caused by subtle interplay between ionic screening and chain entropy.

Conserved noncanonical residue Gly-126 confers instability to the middle part of the tropomyosin molecule

Tropomyosin (Tm) is a two-stranded α-helical coiled-coil protein with a well established role in regulation of actin cytoskeleton and muscle contraction. It is believed that many Tm functions are enabled by its flexibility whose nature has not been completely understood. We hypothesized that the well conserved non-canonical residue Gly-126 causes local destabilization of Tm. To test this, we substituted Gly-126 in skeletal muscle α-Tm either with an Ala residue, which should stabilize the Tm α-helix, or with an Arg residue, which is expected to stabilize both α-helix and coiled-coil structure of Tm. We have shown that both mutations dramatically reduce the rate of Tm proteolysis by trypsin at Asp-133. Differential scanning calorimetry was used for detailed investigation of thermal unfolding of the Tm mutants, both free in solution and bound to F-actin. It was shown that a significant part of wild type Tm unfolds in a non-cooperative manner at low temperature, and both mutations confer cooperativity to this part of the Tm molecule. The size of the flexible middle part of Tm is estimated to be 60-70 amino acid residues, about a quarter of the Tm molecule. Thus, our results show that flexibility is unevenly distributed in the Tm molecule and achieves the highest extent in its middle part. We conclude that the highly conserved Gly-126, acting in concert with the previously identified non-canonical Asp-137, destabilizes the middle part of Tm, resulting in a more flexible region that is important for Tm function.

Oxidation mimicking substitution of conservative cysteine in recoverin suppresses its membrane association

Recoverin belongs to the family of intracellular Ca(2+)-binding proteins containing EF-hand domains, neuronal calcium sensors (NCS). In photoreceptor outer segments, recoverin is involved into the recovery of visual cycle via Ca(2+)-dependent interaction with disk membranes and inhibition of rhodopsin kinase. The function of a conservative within NCS family Cys residue in the inactive EF-loop 1 remains unclear, but previous study has shown its vulnerability to oxidation under mild oxidizing conditions. To elucidate the influence of oxidation of the conservative Cys39 in recoverin the properties of its C39D mutant, mimicking oxidative conversion of Cys39 into sulfenic, sulfinic or sulfonic acids have been studied using intrinsic fluorescence, circular dichroism, and equilibrium centrifugation methods. The C39D substitution results in essential changes in structural, physico-chemical and physiological properties of the protein: it reduces α-helical content, decreases thermal stability and suppresses protein affinity for photoreceptor membranes. The latter effect precludes proper functioning of the Ca(2+)-myristoyl switch in recoverin. The revealed significance of oxidation state of Cys39 for maintaining the protein functional status shows that it may serve as redox sensor in vision and suggests an explanation of the available data on localization and light-dependent translocation of recoverin in rod photoreceptors.

Metal-controlled interdomain cooperativity in parvalbumins

Conformational behavior of five homologous proteins, parvalbumins (PAs) from northern pike (alpha and beta isoforms), Baltic cod, and rat (alpha and beta isoforms), was studied by scanning calorimetry, circular dichroism, and bis-ANS fluorescence. The mechanism of the temperature-induced denaturation of these proteins depends dramatically on both the peculiarities of their amino acid sequences and on their interaction with metal ions. For example, the pike alpha-PA melting can be described by two successive two-state transitions with mid-temperatures of 90 and 120 degrees C, suggesting the presence of two thermodynamic domains. The intermediate state populated at the end of the first transition was shown to bind Ca(2+) ions, and was characterized by the largely preserved secondary structure and increased solvent exposure of hydrophobic groups. Mg(2+)- and Na(+)-loaded forms of pike alpha-PA demonstrated a single two-state transition. Therefore, the mechanism of the PA thermal denaturation is controlled by metal binding. It ranged from the absence of detectable first-order transition (apo-form of pike PA), to the two-state transition (e.g., Mg(2+)- and Na(+)-loaded forms of pike alpha-PA), to the more complex mechanisms (Ca(2+)-loaded PAs) involving at least one partially folded intermediate. Analysis of isolated cavities in the protein structures revealed that the interface between the CD and EF subdomains of Ca(2+)-loaded pike alpha-PA is much more loosely packed compared with PAs manifesting single heat-sorption peak. The impairment of interactions between CD and EF subdomains may cause a loss of structural cooperativity and appearance of two separate thermodynamic domains. One more peculiar feature of pike alpha-PA is that depending on its interactions with metal ions, it can be an intrinsically disordered protein (apo-form), an ordered protein of mesophilic (Na(+)-bound state), thermophilic (Mg(2+)-form), or even of the hyperthermophilic origin (Ca(2+)-form).

Leucine 85 is an important determinant of divalent ion affinity in rat beta-parvalbumin (Oncomodulin)

Despite 69% sequence identity with chicken parvalbumin 3 (CPV3), rat beta-parvalbumin (beta-PV) exhibits a substantially lower Ca(2+) affinity (DeltaDeltaG degrees ' = 2.0 kcal/mol). This difference largely reflects the disparate behavior of the respective CD sites. Replacement of the rat beta-PV codon with the CPV3 codon at positions 49, 50, and 57-60 produces virtual sequence identity with the CPV3 CD site. However, the resulting protein exhibits a modest (0.5 kcal/mol) improvement in Ca(2+) affinity, implying that sequence differences beyond the binding site modulate divalent ion binding behavior. The solution structure of Ca(2+)-free rat beta-PV suggested that Leu-85, phenylalanine in CPV3, might be an important determinant. Therefore, the impact of the L85F mutation on divalent ion affinity was examined in rat beta-PV, in the variant harboring all six of the aforementioned CD site mutations, and in the intermediate CD site variants. We find that the identity of residue 85, located within the E helix, strongly influences divalent ion affinity in the mammalian beta-PV isoform and that its impact is mediated by interactions with residues in the CD site. In the wild-type protein, L85F primarily affects the EF site. By contrast, in the presence of the six CD site mutations, L85F also improves the CD site performance, yielding a protein with Ca(2+) affinity rivaling that of CPV3 and markedly enhanced Mg(2+) affinity as well. The impact of L85F on CD site Ca(2+) affinity is particularly sensitive to the identities of residues 59 and 60. Interestingly, however, significant improvement in CD site Mg(2+) affinity also requires mutation of additional CD site residues.

Structural characteristics of the plasmid-encoded toxin from enteroaggregative Escherichia coli

Intoxication by the plasmid-encoded toxin (Pet) of enteroaggregative Escherichia coli requires toxin translocation from the endoplasmic reticulum (ER) to the cytosol. This event involves the quality control system of ER-associated degradation (ERAD), but the molecular details of the process are poorly characterized. For many structurally distinct AB-type toxins, ERAD-mediated translocation is triggered by the spontaneous unfolding of a thermally unstable A chain. Here we show that Pet, a non-AB toxin, engages ERAD by a different mechanism that does not involve thermal unfolding. Circular dichroism and fluorescence spectroscopy measurements demonstrated that Pet maintains most of its secondary and tertiary structural features at 37 degrees C, with significant thermal unfolding only occurring at temperatures >or=50 degrees C. Fluorescence quenching experiments detected the partial solvent exposure of Pet aromatic amino acid residues at 37 degrees C, and a cell-based assay suggested that these changes could activate an ERAD-related event known as the unfolded protein response. We also found that HEp-2 cells were resistant to Pet intoxication when incubated with glycerol, a protein stabilizer. Altogether, our data are consistent with a model in which ERAD activity is triggered by a subtle structural destabilization of Pet and the exposure of Pet hydrophobic residues at physiological temperature. This was further supported by computer modeling analysis, which identified a surface-exposed hydrophobic loop among other accessible nonpolar residues in Pet. From our data it appears that Pet can promote its ERAD-mediated translocation into the cytosol by a distinct mechanism involving partial exposure of hydrophobic residues rather than the substantial unfolding observed for certain AB toxins.