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1.  Differences in the intrinsic immunogenicity and allergenicity of Bet v 1 and related food allergens revealed by site-directed mutagenesis 
Allergy  2013;69(2):208-215.
Background
Birch pollen allergies are frequently associated with adverse reactions to various fruits, nuts, or vegetables, described as pollen–food syndrome (PFS) and caused by cross-reactive IgE antibodies primarily directed against Bet v 1. Specific immunotherapy (SIT) represents an effective treatment for inhalant allergies; however, successful birch pollen SIT does not correlate well with the amelioration of concomitant food allergies.
Methods
As vaccine candidates, apple Mal d 1 as well as hazelnut Cor a 1 derivatives were designed by in silico backbone analyses of the respective allergens. The proteins were produced by site-directed mutagenesis as fold variants of their parental allergens. Because Mal d 1 and Cor a 1 form cysteine-mediated aggregates, nonaggregative cysteine to serine mutants were also generated. The proteins were characterized physicochemically, immunologically, and in in vivo models with or without adjuvant.
Results
The structurally modified proteins showed significantly decreased IgE binding capacity. Notably, both in vivo models revealed reduced immunogenicity of the hypoallergenic fold variants. When formulated with alum, the monomeric cysteine mutants induced a similar immune response as the aggregated parental allergens, which is in contrast with data published on Bet v 1.
Conclusion
These findings lead to the suggestion that the Bet v 1 structure has unique intrinsic properties, which could account for its high allergenicity. Obviously, these characteristics are not entirely shared with its food homologues from apple and hazelnut. Thus, it is important to tackle pollen-related food allergies from different angles for the generation of effective vaccine candidates to treat birch PFS.
doi:10.1111/all.12306
PMCID: PMC4041322  PMID: 24224690
apple allergy; birch pollen-associated food allergies; hazelnut allergy; pollen–food syndrome; protein remodeling
2.  Towards automated crystallographic structure refinement with phenix.refine  
phenix.refine is a program within the PHENIX package that supports crystallographic structure refinement against experimental data with a wide range of upper resolution limits using a large repertoire of model parameterizations. This paper presents an overview of the major phenix.refine features, with extensive literature references for readers interested in more detailed discussions of the methods.
phenix.refine is a program within the PHENIX package that supports crystallographic structure refinement against experimental data with a wide range of upper resolution limits using a large repertoire of model parameterizations. It has several automation features and is also highly flexible. Several hundred parameters enable extensive customizations for complex use cases. Multiple user-defined refinement strategies can be applied to specific parts of the model in a single refinement run. An intuitive graphical user interface is available to guide novice users and to assist advanced users in managing refinement projects. X-ray or neutron diffraction data can be used separately or jointly in refinement. phenix.refine is tightly integrated into the PHENIX suite, where it serves as a critical component in automated model building, final structure refinement, structure validation and deposition to the wwPDB. This paper presents an overview of the major phenix.refine features, with extensive literature references for readers interested in more detailed discussions of the methods.
doi:10.1107/S0907444912001308
PMCID: PMC3322595  PMID: 22505256
structure refinement; PHENIX; joint X-ray/neutron refinement; maximum likelihood; TLS; simulated annealing; subatomic resolution; real-space refinement; twinning; NCS
3.  Re-refinement from deposited X-ray data can deliver improved models for most PDB entries 
An evaluation of validation and real-space intervention possibilities for improving existing automated (re-)refinement methods.
The deposition of X-ray data along with the customary structural models defining PDB entries makes it possible to apply large-scale re-refinement protocols to these entries, thus giving users the benefit of improvements in X-ray methods that have occurred since the structure was deposited. Auto­mated gradient refinement is an effective method to achieve this goal, but real-space intervention is most often required in order to adequately address problems detected by structure-validation software. In order to improve the existing protocol, automated re-refinement was combined with structure validation and difference-density peak analysis to produce a catalogue of problems in PDB entries that are amenable to automatic correction. It is shown that re-refinement can be effective in producing improvements, which are often associated with the systematic use of the TLS parameterization of B factors, even for relatively new and high-resolution PDB entries, while the accompanying manual or semi-manual map analysis and fitting steps show good prospects for eventual automation. It is proposed that the potential for simultaneous improvements in methods and in re-refinement results be further encouraged by broadening the scope of depositions to include refinement metadata and ultimately primary rather than reduced X-ray data.
doi:10.1107/S0907444908037591
PMCID: PMC2631631  PMID: 19171973
re-refinement
4.  Crystallographically Mapped Ligand Binding Differs in High and Low IgE Binding Isoforms of Birch Pollen Allergen Bet v 1 
Journal of Molecular Biology  2012;422(1):109-123.
The ability of pathogenesis-related proteins of family 10 to bind a broad spectrum of ligands is considered to play a key role for their physiological and pathological functions. In particular, Bet v 1, an archetypical allergen from birch pollen, is described as a highly promiscuous ligand acceptor. However, the detailed recognition mechanisms, including specificity factors discriminating binding properties of naturally occurring Bet v 1 variants, are poorly understood.
Here, we report crystal structures of Bet v 1 variants in complex with an array of ligands at a resolution of up to 1.2 Å. Residue 30 within the hydrophobic pocket not only discriminates in high and low IgE binding Bet v 1 isoforms but also induces a drastic change in the binding mode of the model ligand deoxycholate. Ternary crystal structure complexes of Bet v 1 with several ligands together with the fluorogenic reporter 1-anilino-8-naphthalene sulfonate explain anomalous fluorescence binding curves obtained from 1-anilino-8-naphthalene sulfonate displacement assays. The structures reveal key interaction residues such as Tyr83 and rationalize both the binding specificity and promiscuity of the so-called hydrophobic pocket in Bet v 1.
The intermolecular interactions of Bet v 1 reveal an unexpected complexity that will be indispensable to fully understand its roles within the physiological and allergenic context.
Graphical Abstract
Highlights
► Ligand binding to Bet v 1 may contribute to explain its allergenicity. ► High-resolution structures reveal the binding mode of diverse ligands to Bet v 1. ► Residue 30 starkly influences the binding properties of different Bet v 1 isoforms. ► Ternary complexes with diverse ligands explain anomalous fluorescence binding curves. ► Betv1 isoforms differ in ligand binding, which may translate into their allergenicity.
doi:10.1016/j.jmb.2012.05.016
PMCID: PMC3422537  PMID: 22634284
ANS, 1-anilino-8-naphthalene sulfonate; BRA, brassinolide; DXC, deoxycholate; iDXC, inner deoxycholate; oDXC, outer deoxycholate; LPS, lipopolysaccharide; MPD, 2-methyl-2,4-pentanediol; NDSB-256, non-detergent sulfobetaine 256; PR-10, pathogenesis-related protein 10; PDB, Protein Data Bank; molecular allergenicity; ANS displacement assay; structure–allergenicity relationship; binding specificity and promiscuity; dressed allergens
5.  Detection and correction of underassigned rotational symmetry prior to structure deposition 
An X-ray structural model can be reassigned to a higher symmetry space group using the presented framework if its noncrystallographic symmetry operators are close to being exact crystallographic relationships. About 2% of structures in the Protein Data Bank can be reclassified in this way.
Up to 2% of X-ray structures in the Protein Data Bank (PDB) potentially fit into a higher symmetry space group. Redundant protein chains in these structures can be made compatible with exact crystallographic symmetry with minimal atomic movements that are smaller than the expected range of coordinate uncertainty. The incidence of problem cases is somewhat difficult to define precisely, as there is no clear line between underassigned symmetry, in which the subunit differences are unsupported by the data, and pseudosymmetry, in which the subunit differences rest on small but significant intensity differences in the diffraction pattern. To help catch symmetry-assignment problems in the future, it is useful to add a validation step that operates on the refined coordinates just prior to structure deposition. If redundant symmetry-related chains can be removed at this stage, the resulting model (in a higher symmetry space group) can readily serve as an isomorphous replacement starting point for re-refinement using re-indexed and re-integrated raw data. These ideas are implemented in new software tools available at http://cci.lbl.gov/labelit.
doi:10.1107/S0907444910001502
PMCID: PMC2865365  PMID: 20445225
underassigned rotational symmetry; LABELIT; validation
6.  PDB_REDO: automated re-refinement of X-ray structure models in the PDB 
Journal of Applied Crystallography  2009;42(Pt 3):376-384.
The majority of previously deposited X-ray structures can be improved by applying current refinement methods.
Structural biology, homology modelling and rational drug design require accurate three-dimensional macromolecular coordinates. However, the coordinates in the Protein Data Bank (PDB) have not all been obtained using the latest experimental and computational methods. In this study a method is presented for automated re-refinement of existing structure models in the PDB. A large-scale benchmark with 16 807 PDB entries showed that they can be improved in terms of fit to the deposited experimental X-ray data as well as in terms of geometric quality. The re-refinement protocol uses TLS models to describe concerted atom movement. The resulting structure models are made available through the PDB_REDO databank (http://www.cmbi.ru.nl/pdb_redo/). Grid computing techniques were used to overcome the computational requirements of this endeavour.
doi:10.1107/S0021889809008784
PMCID: PMC3246819  PMID: 22477769
X-ray crystallography; refinement; structure validation; Protein Data Bank; grid computing
7.  PDB_REDO: constructive validation, more than just looking for errors 
The decision-making algorithms and software used in PDB_REDO to re-refine and rebuild crystallographic protein structures in the PDB are presented and discussed.
Developments of the PDB_REDO procedure that combine re-refinement and rebuilding within a unique decision-making framework to improve structures in the PDB are presented. PDB_REDO uses a variety of existing and custom-built software modules to choose an optimal refinement protocol (e.g. anisotropic, isotropic or overall B-factor refinement, TLS model) and to optimize the geometry versus data-refinement weights. Next, it proceeds to rebuild side chains and peptide planes before a final optimization round. PDB_REDO works fully automatically without the need for intervention by a crystallographic expert. The pipeline was tested on 12 000 PDB entries and the great majority of the test cases improved both in terms of crystallographic criteria such as R free and in terms of widely accepted geometric validation criteria. It is concluded that PDB_REDO is useful to update the otherwise ‘static’ structures in the PDB to modern crystallographic standards. The publically available PDB_REDO database provides better model statistics and contributes to better refinement and validation targets.
doi:10.1107/S0907444911054515
PMCID: PMC3322608  PMID: 22505269
validation; refinement; model building; automation; PDB
8.  The Bet v 1 fold: an ancient, versatile scaffold for binding of large, hydrophobic ligands 
Background
The major birch pollen allergen, Bet v 1, is a member of the ubiquitous PR-10 family of plant pathogenesis-related proteins. In recent years, a number of diverse plant proteins with low sequence similarity to Bet v 1 was identified. In addition, determination of the Bet v 1 structure revealed the existence of a large superfamily of structurally related proteins. In this study, we aimed to identify and classify all Bet v 1-related structures from the Protein Data Bank and all Bet v 1-related sequences from the Uniprot database.
Results
Structural comparisons of representative members of already known protein families structurally related to Bet v 1 with all entries of the Protein Data Bank yielded 47 structures with non-identical sequences. They were classified into eleven families, five of which were newly identified and not included in the Structural Classification of Proteins database release 1.71. The taxonomic distribution of these families extracted from the Pfam protein family database showed that members of the polyketide cyclase family and the activator of Hsp90 ATPase homologue 1 family were distributed among all three superkingdoms, while members of some bacterial families were confined to a small number of species. Comparison of ligand binding activities of Bet v 1-like superfamily members revealed that their functions were related to binding and metabolism of large, hydrophobic compounds such as lipids, hormones, and antibiotics. Phylogenetic relationships within the Bet v 1 family, defined as the group of proteins with significant sequence similarity to Bet v 1, were determined by aligning 264 Bet v 1-related sequences. A distance-based phylogenetic tree yielded a classification into 11 subfamilies, nine exclusively containing plant sequences and two subfamilies of bacterial proteins. Plant sequences included the pathogenesis-related proteins 10, the major latex proteins/ripening-related proteins subfamily, and polyketide cyclase-like sequences.
Conclusion
The ubiquitous distribution of Bet v 1-related proteins among all superkingdoms suggests that a Bet v 1-like protein was already present in the last universal common ancestor. During evolution, this protein diversified into numerous families with low sequence similarity but with a common fold that succeeded as a versatile scaffold for binding of bulky ligands.
doi:10.1186/1471-2148-8-286
PMCID: PMC2577659  PMID: 18922149
9.  471 IgE from Birch Pollen Allergic Patients Cross-reacts with Two Distinct Bet V 1 Related Proteins in Mung Beans: VIG R 1 and Cytokinin-specific Binding Protein 
The World Allergy Organization Journal  2012;5(Suppl 2):S166-S167.
Background
Mung beans (Vigna radiata) contain 2 Bet v 1 related proteins: Vig r 1, a member of the PR-10 subfamily, and cytokinin-specific binding protein (CSBP), a protein with low sequence identity (31%) to Bet v 1. We aimed to compare Vig r 1 and CSBP to Bet v 1 regarding biochemical and immunological properties.
Methods
Percent surface identity between Bet v 1, CSBP and Vig r 1 was calculated based on structural alignments using an algorithm considering backbone conformations and identities of aligned residues. The allergens were expressed in Escherichia coli and purified by metal chelate affinity and ion exchange chromatography. Secondary structures were compared using circular dichroism (CD) spectroscopy. Binding and cross-reactivity of IgE from Bet v 1-sensitized patients' sera to rCSBP, rVig r 1.0101 and rBet v 1.0101 were examined by ELISA and ELISA inhibition.
Results
Structural comparison of the 3 proteins revealed that 29% of the solvent-accessible surface area of CSBP was identical to Bet v 1, while Vig r 1 and Bet v 1 shared 50% surface area. In addition, 2 surface patches, conserved between Bet v 1 and CSBP, were identified as potential cross-reactive epitopes. 30% and 79% of Bet v 1-sensitized birch pollen allergic patients' sera (n = 33) showed IgE binding to CSBP and Vig r 1, respectively. Of 12 Bet v 1-sensitized patients, who reported reactions or had positive prick-to-prick tests to mung bean sprouts, 10 showed IgE binding to Vig r 1 and 7 to CSBP. Bet v 1 completely inhibited IgE binding to CSBP and Vig r 1. Furthermore, CSBP showed inhibitory activity on IgE binding to Vig r 1 and vice versa.
Conclusions
This study demonstrates IgE cross-reactivity between Bet v 1 and CSBP, despite their low sequence identity. In addition to Vig r 1, a PR-10 subfamily member, IgE binding to CSBP might contribute to allergic reactions in mung bean sprouts.
doi:10.1097/01.WOX.0000411586.57163.22
PMCID: PMC3512672
10.  Allergen hybrids – next generation vaccines for Fagales pollen immunotherapy 
Summary
Background
Trees belonging to the order of Fagales show a distinct geographical distribution. While alder and birch are endemic in the temperate zones of the Northern Hemisphere, hazel, hornbeam and oak prefer a warmer climate. However, specific immunotherapy of Fagales pollen-allergic patients is mainly performed using birch pollen extracts, thus limiting the success of this intervention in birch-free areas.
Objectives
T cells are considered key players in the modification of an allergic immune response during specific immunotherapy (SIT), therefore we thought to combine linear T cell epitope-containing stretches of the five most important Fagales allergens from birch, hazel, alder, oak and hornbeam resulting in a Fagales pollen hybrid (FPH) molecule applicable for SIT.
Methods
A Fagales pollen hybrid was generated by PCR-based recombination of low IgE-binding allergen epitopes. Moreover, a structural-variant FPH4 was calculated by in silico mutagenesis, rendering the protein unable to adopt the Bet v 1-like fold. Both molecules were produced in Escherichia coli, characterized physico-chemically as well as immunologically, and tested in mouse models of allergic sensitization as well as allergy prophylaxis.
Results
Using spectroscopic analyses, both proteins were monomeric, and the secondary structure elements of FPH resemble the ones typical for Bet v 1-like proteins, whereas FPH4 showed increased amounts of unordered structure. Both molecules displayed reduced binding capacities of Bet v 1-specific IgE antibodies. However, in a mouse model, the proteins were able to induce high IgG titres cross-reactive with all parental allergens. Moreover, prophylactic treatment with the hybrid proteins prevented pollen extract-induced allergic lung inflammation in vivo.
Conclusion
The hybrid molecules showed a more efficient uptake and processing by dendritic cells resulting in a modified T cell response. The proteins had a lower IgE-binding capacity compared with the parental allergens, thus the high safety profile and increased efficacy emphasize clinical application for the treatment of Fagales multi-sensitization.
doi:10.1111/cea.12250
PMCID: PMC4041320  PMID: 24330218
allergen-specific immunotherapy; birch pollen allergy; Fagales pollen allergy; hybrid protein; immunomodulation; protein remodelling
11.  Structure of the Archaeoglobus fulgidus orphan ORF AF1382 determined by sulfur SAD from a moderately diffracting crystal 
The crystal structure of the 11.14 kDa orphan ORF 1382 from Archaeoglobus fulgidus (AF1382) has been determined by sulfur SAD phasing using data collected from a moderately diffracting crystal and 1.9 Å synchrotron X-rays.
The crystal structure of the 11.14 kDa orphan ORF 1382 from Archaeoglobus fulgidus (AF1382) has been determined by sulfur SAD phasing using a moderately diffracting crystal and 1.9 Å wavelength synchrotron X-rays. AF1382 was selected as a structural genomics target by the Southeast Collaboratory for Structural Genomics (SECSG) since sequence analyses showed that it did not belong to the Pfam-A database and thus could represent a novel fold. The structure was determined by exploiting longer wavelength X-rays and data redundancy to increase the anomalous signal in the data. AF1382 is a 95-­residue protein containing five S atoms associated with four methionine residues and a single cysteine residue that yields a calculated Bijvoet ratio (ΔF anom/F) of 1.39% for 1.9 Å wavelength X-rays. Coupled with an average Bijvoet redundancy of 25 (two 360° data sets), this produced an excellent electron-density map that allowed 69 of the 95 residues to be automatically fitted. The S-SAD model was then manually completed and refined (R = 23.2%, R free = 26.8%) to 2.3 Å resolution (PDB entry 3o3k). High-resolution data were subsequently collected from a better diffracting crystal using 0.97 Å wavelength synchrotron X-rays and the S-SAD model was refined (R = 17.9%, R free = 21.4%) to 1.85 Å resolution (PDB entry 3ov8). AF1382 has a winged-helix–turn–helix structure common to many DNA-binding proteins and most closely resembles the N-terminal domain (residues 1–82) of the Rio2 kinase from A. fulgidus, which has been shown to bind DNA, and a number of MarR-family transcriptional regulators, suggesting a similar DNA-binding function for AF1382. The analysis also points out the advantage gained from carrying out data reduction and structure determination on-site while the crystal is still available for further data collection.
doi:10.1107/S0907444912026212
PMCID: PMC3489105  PMID: 22948926
AF1382; orphan ORFs; sulfur SAD; Archaeoglobus fulgidus
12.  The good, the bad and the dubious: VHELIBS, a validation helper for ligands and binding sites 
Background
Many Protein Data Bank (PDB) users assume that the deposited structural models are of high quality but forget that these models are derived from the interpretation of experimental data. The accuracy of atom coordinates is not homogeneous between models or throughout the same model. To avoid basing a research project on a flawed model, we present a tool for assessing the quality of ligands and binding sites in crystallographic models from the PDB.
Results
The Validation HElper for LIgands and Binding Sites (VHELIBS) is software that aims to ease the validation of binding site and ligand coordinates for non-crystallographers (i.e., users with little or no crystallography knowledge). Using a convenient graphical user interface, it allows one to check how ligand and binding site coordinates fit to the electron density map. VHELIBS can use models from either the PDB or the PDB_REDO databank of re-refined and re-built crystallographic models. The user can specify threshold values for a series of properties related to the fit of coordinates to electron density (Real Space R, Real Space Correlation Coefficient and average occupancy are used by default). VHELIBS will automatically classify residues and ligands as Good, Dubious or Bad based on the specified limits. The user is also able to visually check the quality of the fit of residues and ligands to the electron density map and reclassify them if needed.
Conclusions
VHELIBS allows inexperienced users to examine the binding site and the ligand coordinates in relation to the experimental data. This is an important step to evaluate models for their fitness for drug discovery purposes such as structure-based pharmacophore development and protein-ligand docking experiments.
doi:10.1186/1758-2946-5-36
PMCID: PMC3733808  PMID: 23895374
Electron density map; Binding site structure validation; Ligand structure validation; Protein structure validation; PDB; PDB_REDO
13.  Dissection of immunoglobulin E and T lymphocyte reactivity of isoforms of the major birch pollen allergen Bet v 1: potential use of hypoallergenic isoforms for immunotherapy 
We dissected the T cell activation potency and the immunoglobulin (Ig) E-binding properties (allergenicity) of nine isoforms of Bet v 1 (Bet v 1a-Bet v 1l), the major birch pollen allergen. Immunoblot experiments showed that Bet v 1 isoforms differ in their ability to bind IgE from birch pollen-allergic patients. All patients tested displayed similar IgE-binding patterns toward each particular isoform. Based on these experiments, we grouped Bet v 1 isoforms in three classes: molecules with high IgE-binding activity (isoforms a, e, and j), intermediate IgE- binding (isoforms b, c, and f), and low/no IgE-binding activity (isoforms d, g, and 1). Bet v 1a, a recombinant isoform selected from a cDNA expression library using IgE immunoscreening exhibited the highest IgE-binding activity. Isoforms a, b, d, e, and 1 were chosen as representatives from the three classes for experimentation. The potency of each isoallergen to activate T lymphocytes from birch pollen- allergic patients was assayed using peripheral blood mononuclear cells, allergen-specific T cell lines, and peptide-mapped allergen-specific T cell clones. Among the patients, some displayed a broad range of T cell- recognition patterns for Bet v 1 isoforms whereas others seemed to be restricted to particular isoforms. In spite of this variability, the highest scores for T cell proliferative responses were observed with isoform d (low IgE binder), followed by b, 1, e, and a. In vivo (skin prick) tests showed that the potency of isoforms d and 1 to induce typical urticarial type 1 reactions in Bet v 1-allergic individuals was significantly lower than for isoforms a, b, and e. Taken together, our results indicate that hypoallergenic Bet v 1 isoforms are potent activators of allergen-specific T lymphocytes, and Bet v 1 isoforms with high in vitro IgE-binding activity and in vivo allergenicity can display low T cell antigenicity. Based on these findings, we propose a novel approach for immunotherapy of type I allergies: a treatment with high doses of hypoallergenic isoforms or recombinant variants of atopic allergens. We proceed on the assumption that this measure would modulate the quality of the T helper cell response to allergens in vivo. The therapy form would additionally implicate a reduced risk of anaphylactic side effects.
PMCID: PMC2192443  PMID: 8627171
14.  Prevention of Birch Pollen-Related Food Allergy by Mucosal Treatment with Multi-Allergen-Chimers in Mice 
PLoS ONE  2012;7(6):e39409.
Background
Among birch pollen allergic patients up to 70% develop allergic reactions to Bet v 1-homologue food allergens such as Api g 1 (celery) or Dau c 1 (carrot), termed as birch pollen-related food allergy. In most cases, specific immunotherapy with birch pollen extracts does not reduce allergic symptoms to the homologue food allergens. We therefore genetically engineered a multi-allergen chimer and tested if mucosal treatment with this construct could represent a novel approach for prevention of birch pollen-related food allergy.
Methodology
BALB/c mice were poly-sensitized with a mixture of Bet v 1, Api g 1 and Dau c 1 followed by a sublingual challenge with carrot, celery and birch pollen extracts. For prevention of allergy sensitization an allergen chimer composed of immunodominant T cell epitopes of Api g 1 and Dau c 1 linked to the whole Bet v 1 allergen, was intranasally applied prior to sensitization.
Results
Intranasal pretreatment with the allergen chimer led to significantly decreased antigen-specific IgE-dependent β-hexosaminidase release, but enhanced allergen-specific IgG2a and IgA antibodies. Accordingly, IL-4 levels in spleen cell cultures and IL-5 levels in restimulated spleen and cervical lymph node cell cultures were markedly reduced, while IFN-γ levels were increased. Immunomodulation was associated with increased IL-10, TGF-β and Foxp3 mRNA levels in NALT and Foxp3 in oral mucosal tissues. Treatment with anti-TGF-β, anti-IL10R or anti-CD25 antibodies abrogated the suppression of allergic responses induced by the chimer.
Conclusion
Our results indicate that mucosal application of the allergen chimer led to decreased Th2 immune responses against Bet v 1 and its homologue food allergens Api g 1 and Dau c 1 by regulatory and Th1-biased immune responses. These data suggest that mucosal treatment with a multi-allergen vaccine could be a promising treatment strategy to prevent birch pollen-related food allergy.
doi:10.1371/journal.pone.0039409
PMCID: PMC3387141  PMID: 22768077
15.  117 Allergy is an Epithelial Barrier Disease 
Background
The purpose of this study is to explore the role of epithelium in acute allergic diseases.
Methods
Birch pollen allergic patients and healthy control subjects were recruited. In vivo nasal pollen challenges were performed and nasal epithelial specimens were collected. A systems biology approach using a wealth of methods, including several microscopy techniques (light, confocal, immuno transmission electron [TEM]), transcriptomics (chips and massive parallel sequencing), mass spectrometry, immunohistology, in silico analyses were used.
Results
Already 1 minute after the birch pollen perturbation Bet v 1 was found both on cell surfaces as well as within villae, in cytoplasm, in intracellular vesicles, and also in nuclei of epithelial cells in allergic patients, but not in the healthy individuals. Anti-Bet v 1 stainings in conjunctival biopsies supported a very rapid traffic through the epithelium in allergic patients, but not in healthy subjects. A striking specificity is observed when birch pollen allergic subjects were also challenged with timothy grass pollen and no entry of this pollen allergen Phl p 1 into epithelial cells was detected. While the specific transport mechanism for birch pollen remains unsolved the first hints of the role of caveolae in this have been obtained. In the double immunoTEM analyses caveolin 2, but not caveolin 1 or 3, was present on the conjunctival epithelial surface in the same clusters as Bet v 1. Transcriptomics indicated that the health epithelium displayed a strong immune response against pollen allergens while this response was absent in the epithelium of allergic patients.
Conclusions
Active transport of allergens through the epithelium might be incorporated to the pathogenesis of allergy. It is possible that the healthy epithelium displays a strong immune response against pollen allergens and thus escapes from becoming allergic. If allergy turns out to be, at least in part, a result of epithelial hyposensitivity, it could have major consequences in the strategies of prevention and treatment of these diseases. Towards this end, a national allergy program has been launched in Finland, which changes the basic idea of trying to avoid allergens to the concept of natural exposure and tolerance.
doi:10.1097/01.WOX.0000411862.58879.ac
PMCID: PMC3512654
16.  A multivariate likelihood SIRAS function for phasing and model refinement 
The application of a multivariate likelihood function to a single isomorphous replacement with anomalous scattering experiment improves phasing and automated model building with iterative refinement in the test cases shown.
A likelihood function based on the multivariate probability distribution of all observed structure-factor amplitudes from a single isomorphous replacement with anomalous scattering experiment has been derived and implemented for use in substructure refinement and phasing as well as macromolecular model refinement. Efficient calculation of a multidimensional integration required for function evaluation has been achieved by approximations based on the function’s properties. The use of the function in both phasing and protein model building with iterative refinement was essential for successful automated model building in the test cases presented.
doi:10.1107/S0907444909028078
PMCID: PMC2748965  PMID: 19770502
multivariate normal probability distribution; single isomorphous replacement with anomalous scattering; experimental phasing; direct incorporation of prior phase information
17.  On the use of logarithmic scales for analysis of diffraction data 
Conventional and free R factors and their difference, as well as the ratio of the number of measured reflections to the number of atoms in the crystal, were studied as functions of the resolution at which the structures were reported. When the resolution was taken uniformly on a logarithmic scale, the most frequent values of these functions were quasi-linear over a large resolution range.
Predictions of the possible model parameterization and of the values of model characteristics such as R factors are important for macromolecular refinement and validation protocols. One of the key parameters defining these and other values is the resolution of the experimentally measured diffraction data. The higher the resolution, the larger the number of diffraction data N ref, the larger its ratio to the number N at of non-H atoms, the more parameters per atom can be used for modelling and the more precise and detailed a model can be obtained. The ratio N ref/N at was calculated for models deposited in the Protein Data Bank as a function of the resolution at which the structures were reported. The most frequent values for this distribution depend essentially linearly on resolution when the latter is expressed on a uniform logarithmic scale. This defines simple analytic formulae for the typical Matthews coefficient and for the typically allowed number of parameters per atom for crystals diffracting to a given resolution. This simple dependence makes it possible in many cases to estimate the expected resolution of the experimental data for a crystal with a given Matthews coefficient. When expressed using the same logarithmic scale, the most frequent values for R and R free factors and for their difference are also essentially linear across a large resolution range. The minimal R-factor values are practically constant at resolutions better than 3 Å, below which they begin to grow sharply. This simple dependence on the resolution allows the prediction of expected R-factor values for unknown structures and may be used to guide model refinement and validation.
doi:10.1107/S0907444909039638
PMCID: PMC2789003  PMID: 19966414
resolution; logarithmic scale; R factor; data-to-parameter ratio
18.  What can we learn by computing 13Cα chemical shifts for X-ray protein models? 
The room-temperature X-ray structures of two proteins, solved at 1.8 and 1.9 Å resolution, are used to investigate whether a set of conformations, rather than a single X-ray structure, provides better agreement with both the X-ray data and the observed 13Cα chemical shifts in solution.
The room-temperature X-ray structures of ubiquitin (PDB code 1ubq) and of the RNA-binding domain of nonstructural protein 1 of influenza A virus (PDB code 1ail) solved at 1.8 and 1.9 Å resolution, respectively, were used to investigate whether a set of conformations rather than a single X-ray structure provides better agreement with both the X-ray data and the observed 13Cα chemical shifts in solution. For this purpose, a set of new conformations for each of these proteins was generated by fitting them to the experimental X-ray data deposited in the PDB. For each of the generated structures, which show R and R free factors similar to those of the deposited X-ray structure, the 13Cα chemical shifts of all residues in the sequence were computed at the DFT level of theory. The sets of conformations were then evaluated by their ability to reproduce the observed 13Cα chemical shifts by using the conformational average root-mean-square-deviation (ca-r.m.s.d.). For ubiquitin, the computed set of conformations is a better representation of the observed 13Cα chemical shifts in terms of the ca-r.m.s.d. than a single X-ray-derived structure. However, for the RNA-binding domain of nonstructural protein 1 of influenza A virus, consideration of an ensemble of conformations does not improve the agreement with the observed 13Cα chemical shifts. Whether an ensemble of conformations rather than any single structure is a more accurate representation of a protein structure in the crystal as well as of the observed 13Cα chemical shifts is determined by the dispersion of coordinates, in terms of the all-atom r.m.s.d. among the generated models; these generated models satisfy the experimental X-ray data with accuracy as good as the PDB structure. Therefore, generation of an ensemble is a necessary step to determine whether or not a single structure is sufficient for an accurate representation of both experimental X-ray data and observed 13Cα chemical shifts in solution.
doi:10.1107/S0907444909012086
PMCID: PMC2703576  PMID: 19564690
13C chemical shifts
19.  CaspR: a web server for automated molecular replacement using homology modelling 
Nucleic Acids Research  2004;32(Web Server issue):W606-W609.
Molecular replacement (MR) is the method of choice for X-ray crystallography structure determination when structural homologues are available in the Protein Data Bank (PDB). Although the success rate of MR decreases sharply when the sequence similarity between template and target proteins drops below 35% identical residues, it has been found that screening for MR solutions with a large number of different homology models may still produce a suitable solution where the original template failed. Here we present the web tool CaspR, implementing such a strategy in an automated manner. On input of experimental diffraction data, of the corresponding target sequence and of one or several potential templates, CaspR executes an optimized molecular replacement procedure using a combination of well-established stand-alone software tools. The protocol of model building and screening begins with the generation of multiple structure–sequence alignments produced with T-COFFEE, followed by homology model building using MODELLER, molecular replacement with AMoRe and model refinement based on CNS. As a result, CaspR provides a progress report in the form of hierarchically organized summary sheets that describe the different stages of the computation with an increasing level of detail. For the 10 highest-scoring potential solutions, pre-refined structures are made available for download in PDB format. Results already obtained with CaspR and reported on the web server suggest that such a strategy significantly increases the fraction of protein structures which may be solved by MR. Moreover, even in situations where standard MR yields a solution, pre-refined homology models produced by CaspR significantly reduce the time-consuming refinement process. We expect this automated procedure to have a significant impact on the throughput of large-scale structural genomics projects. CaspR is freely available at http://igs-server.cnrs-mrs.fr/Caspr/.
doi:10.1093/nar/gkh400
PMCID: PMC441538  PMID: 15215460
20.  23 Grafting of BET V 1 Epitopes onto its Homologue API G 1 Reveals Patient-Specific IgE Recognition Profiles 
Background
Up to 70% of birch pollen-allergic individuals show adverse reactions to certain plant foods. This cross-reactivity is caused by sensitisation to the major birch pollen allergen Bet v 1 and binding of Bet v 1-specific IgE antibodies to homologous plant food allergens. We aimed to assess the importance of selected conformational epitopes for IgE binding to Bet v 1.
Methods
Chimeras of Bet v 1.0101 and its homologue Api g 1.0101 were constructed. In each of the 4 chimeras, roughly one fourth of the surface residues of Api g 1.0101 were replaced by corresponding residues of Bet v 1.0101. The proteins were expressed in Escherichia coli and purified by chromatographic methods. Secondary structures were checked by CD-spectroscopy. IgE ELISA with Bet v 1.0101, Api g 1.0101 and the chimeras were performed with sera of 63 Bet v 1-sensitized birch pollen allergic patients. For inhibition ELISAs, chimeras were coated and inhibition was performed with the chimeras or Api g 1.0101.
Results
IgE binding to Api g 1.0101, Api-Bet-1, -2, -3 and -4 was observed for 22, 81, 79, 70 and 38% of the sera, respectively. To assess the relevance of the grafted regions for IgE binding to Bet v 1, the amounts of IgE binding to the chimeras were compared with those to Api g 1.0101. Most of the sera recognised either 3 chimeras (39%) or all 4 chimeras (21%) better than Api g 1.0101. Only a minority of the sera showed increased binding to a single chimera. Inhibition ELISAs confirmed the presence of IgE specific for the grafted regions.
Conclusions
Our study indicates that the epitope recognition profile of Bet v 1-specific IgE is highly patient specific. Due to the different IgE binding patterns to Bet v 1, determined by binding of IgE to different chimeras, the existence of a single major IgE epitope on Bet v 1 can be excluded. Moreover, the Bet v 1-specific IgE repertoire is polyclonal and the IgE epitopes are distributed over the whole surface of Bet v 1.
doi:10.1097/01.WOX.0000411768.37811.d5
PMCID: PMC3513146
21.  Perinatal Maternal Administration of Lactobacillus paracasei NCC 2461 Prevents Allergic Inflammation in a Mouse Model of Birch Pollen Allergy 
PLoS ONE  2012;7(7):e40271.
Background
The hygiene hypothesis implies that microbial agents including probiotic bacteria may modulate foetal/neonatal immune programming and hence offer effective strategies for primary allergy prevention; however their mechanisms of action are poorly understood. We investigated whether oral administration of Lactobacillus paracasei NCC 2461 to mothers during gestation/lactation can protect against airway inflammation in offspring in a mouse model of birch pollen allergy, and examined the immune mechanisms involved.
Methods
BALB/c mice were treated daily with L. paracasei in drinking water or drinking water alone in the last week of gestation and during lactation. Their offspring were sensitized with recombinant Bet v 1, followed by aerosol challenge with birch pollen extract.
Results
Maternal exposure to L. paracasei prevented the development of airway inflammation in offspring, as demonstrated by attenuation of eosinophil influx in the lungs; reduction of IL-5 levels in bronchoalveolar lavage, and in lung and mediastinal lymph node cell cultures; and reduced peribronchial inflammatory infiltrate and mucus hypersecretion. While allergen-specific IgE and IgG antibody levels remained unchanged by the treatment, IL-4 and IL-5 production in spleen cell cultures were significantly reduced upon allergen stimulation in offspring of L. paracasei treated mice. Offspring of L. paracasei supplemented mothers had significantly reduced Bet v 1-specific as well as Concanavalin A-induced responses in spleen and mesenteric lymph node cell cultures, suggesting the modulation of both antigen-specific and mitogen-induced immune responses in offspring. These effects were associated with increased Foxp3 mRNA expression in the lungs and increased TGF-beta in serum.
Conclusion
Our data show that in a mouse model of birch pollen allergy, perinatal administration of L. paracasei NCC 2461 to pregnant/lactating mothers protects against the development of airway inflammation in offspring by activating regulatory pathways, likely through TLR2/4 signalling.
doi:10.1371/journal.pone.0040271
PMCID: PMC3391241  PMID: 22792257
22.  PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB) in 2003 
Nucleic Acids Research  2003;31(1):492-493.
PDB-REPRDB is a database of representative protein chains from the Protein Data Bank (PDB). Started at the Real World Computing Partnership (RWCP) in August 1997, it developed to the present system of PDB-REPRDB. In April 2001, the system was moved to the Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST) (http://www.cbrc.jp/); it is available at http://www.cbrc.jp/pdbreprdb/. The current database includes 33 368 protein chains from 16 682 PDB entries (1 September, 2002), from which are excluded (a) DNA and RNA data, (b) theoretically modeled data, (c) short chains (1<40 residues), or (d) data with non-standard amino acid residues at all residues.
The number of entries including membrane protein structures in the PDB has increased rapidly with determination of numbers of membrane protein structures because of improved X-ray crystallography, NMR, and electron microscopic experimental techniques. Since many protein structure studies must address globular and membrane proteins separately, this new elimination factor, which excludes membrane protein chains, is introduced in the PDB-REPRDB system. Moreover, the PDB-REPRDB system for membrane protein chains begins at the same URL. The current membrane database includes 551 protein chains, including membrane domains in the SCOP database of release 1.59 (15 May, 2002).
PMCID: PMC165469  PMID: 12520060
23.  A general method for the unbiased improvement of solution NMR structures by the use of related X-Ray data, the AUREMOL-ISIC algorithm 
Background
Rapid and accurate three-dimensional structure determination of biological macromolecules is mandatory to keep up with the vast progress made in the identification of primary sequence information. During the last few years the amount of data deposited in the protein data bank has substantially increased providing additional information for novel structure determination projects. The key question is how to combine the available database information with the experimental data of the current project ensuring that only relevant information is used and a correct structural bias is produced. For this purpose a novel fully automated algorithm based on Bayesian reasoning has been developed. It allows the combination of structural information from different sources in a consistent way to obtain high quality structures with a limited set of experimental data. The new ISIC (Intelligent Structural Information Combination) algorithm is part of the larger AUREMOL software package.
Results
Our new approach was successfully tested on the improvement of the solution NMR structures of the Ras-binding domain of Byr2 from Schizosaccharomyces pombe, the Ras-binding domain of RalGDS from human calculated from a limited set of NMR data, and the immunoglobulin binding domain from protein G from Streptococcus by their corresponding X-ray structures. In all test cases clearly improved structures were obtained. The largest danger in using data from other sources is a possible bias towards the added structure. In the worst case instead of a refined target structure the structure from the additional source is essentially reproduced. We could clearly show that the ISIC algorithm treats these difficulties properly.
Conclusion
In summary, we present a novel fully automated method to combine strongly coupled knowledge from different sources. The combination with validation tools such as the calculation of NMR R-factors strengthens the impact of the method considerably since the improvement of the structures can be assessed quantitatively. The ISIC method can be applied to a large number of similar problems where the quality of the obtained three-dimensional structures is limited by the available experimental data like the improvement of large NMR structures calculated from sparse experimental data or the refinement of low resolution X-ray structures. Also structures may be refined using other available structural information such as homology models.
doi:10.1186/1472-6807-6-14
PMCID: PMC1559696  PMID: 16800891
24.  Crystallization, dehydration and experimental phasing of WbdD, a bifunctional kinase and methyltransferase from Escherichia coli O9a 
The optimization of WbdD crystals using a novel dehydration protocol and experimental phasing at 3.5 Å resolution by cross-crystal averaging followed by molecular replacement of electron density into a non-isomorphous 3.0 Å resolution native data set are reported.
WbdD is a bifunctional kinase/methyltransferase that is responsible for regulation of lipopolysaccharide O antigen polysaccharide chain length in Escherichia coli serotype O9a. Solving the crystal structure of this protein proved to be a challenge because the available crystals belonging to space group I23 only diffracted to low resolution (>95% of the crystals diffracted to resolution lower than 4 Å and most only to 8 Å) and were non-isomorphous, with changes in unit-cell dimensions of greater than 10%. Data from a serendipitously found single native crystal that diffracted to 3.0 Å resolution were non-isomorphous with a lower (3.5 Å) resolution selenomethionine data set. Here, a strategy for improving poor (3.5 Å resolution) initial phases by density modification and cross-crystal averaging with an additional 4.2 Å resolution data set to build a crude model of WbdD is desribed. Using this crude model as a mask to cut out the 3.5 Å resolution electron density yielded a successful molecular-replacement solution of the 3.0 Å resolution data set. The resulting map was used to build a complete model of WbdD. The hydration status of individual crystals appears to underpin the variable diffraction quality of WbdD crystals. After the initial structure had been solved, methods to control the hydration status of WbdD were developed and it was thus possible to routinely obtain high-resolution diffraction (to better than 2.5 Å resolution). This novel and facile crystal-dehydration protocol may be useful for similar challenging situations.
doi:10.1107/S0907444912029599
PMCID: PMC3447403  PMID: 22993091
WbdD; crystal dehydration
25.  TAP score: torsion angle propensity normalization applied to local protein structure evaluation 
BMC Bioinformatics  2007;8:155.
Background
Experimentally determined protein structures may contain errors and require validation. Conformational criteria based on the Ramachandran plot are mainly used to distinguish between distorted and adequately refined models. While the readily available criteria are sufficient to detect totally wrong structures, establishing the more subtle differences between plausible structures remains more challenging.
Results
A new criterion, called TAP score, measuring local sequence to structure fitness based on torsion angle propensities normalized against the global minimum and maximum is introduced. It is shown to be more accurate than previous methods at estimating the validity of a protein model in terms of commonly used experimental quality parameters on two test sets representing the full PDB database and a subset of obsolete PDB structures. Highly selective TAP thresholds are derived to recognize over 90% of the top experimental structures in the absence of experimental information. Both a web server and an executable version of the TAP score are available at .
Conclusion
A novel procedure for energy normalization (TAP) has significantly improved the possibility to recognize the best experimental structures. It will allow the user to more reliably isolate problematic structures in the context of automated experimental structure determination.
doi:10.1186/1471-2105-8-155
PMCID: PMC1878508  PMID: 17504537

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