scholarly journals NMR resonance assignments of the four isoforms of the hazelnut allergen Cor a 1.04

2019 ◽  
Vol 14 (1) ◽  
pp. 45-49 ◽  
Author(s):  
Sebastian Führer ◽  
Ricarda Zeindl ◽  
Martin Tollinger
Keyword(s):  
Fruits And Vegetables ◽  
Chemical Shifts ◽  
Three Dimensional ◽  
Resonance Assignments ◽  
Subsequent Development ◽  
Dimensional Structure ◽  
Side Chain ◽  
Bet V 1 ◽  
Chemical Shift Data ◽  
Α Helix

Abstract In large parts of Europe, Northern America and China people are suffering from allergies after consuming certain kinds of fruits and vegetables. Typical allergic symptoms range from scratching and itching of the throat to severe symptoms like rhino conjunctivitis and anaphylaxis. For hazelnuts (Corylus avellana), these allergies result from initial sensitization to the birch (Betula verrucosa) pollen allergen Bet v 1 and subsequent development of allergic cross-reactions to proteins that are similar in their three-dimensional structure to the sensitizing protein Bet v 1. The cross-reactive proteins in hazelnut are the four isoforms Cor a 1.04 with a molecular weight of about 17.5 kDa. Significant differences regarding the immunologic behavior of these proteins have been reported. In this work we assigned backbone and side chain 1H, 13C, and 15N chemical shifts of these four isoforms, Cor a 1.0401, Cor a 1.0402, Cor a 1.0403, and Cor a 1.0404 by solution NMR spectroscopy. The chemical shift data confirm the characteristic Bet v onefold for all four isoforms, consisting of seven β-strands that are separated by two short α-helices, along with a long C-terminal α-helix. These data provide the basis for a comparative structural and dynamic analysis of these proteins by NMR in order to characterize their different immunologic cross-reactivities on a molecular level.

scholarly journals Conformation and membrane interaction studies of the potent antimicrobial and anticancer peptide palustrin-Ca

2021 ◽  
Author(s):  
Patrick Brendan Timmons ◽  
Chandralal M Hewage
Keyword(s):  
Sodium Dodecyl ◽  
Three Dimensional ◽  
Dynamics Simulation ◽  
Peptide Sequence ◽  
Helical Conformation ◽  
Dimensional Structure ◽  
Amino Acid Residues ◽  
Anticancer Activities ◽  
American Bullfrog ◽  
Α Helix

Palustrin-Ca (GFLDIIKDTGKEFAVKILNNLKCKLAGGCPP) is a host defense peptide with potent antimicrobial and anticancer activities, first isolated from the skin of the American bullfrog Lithobates catesbeianus. The peptide is 31 amino acid residues long, cationic and amphipathic. Two-dimensional NMR spectroscopy was employed to characterise its three-dimensional structure in a 50/50% water/2,2,2-trifluoroethanol-d3 mixture. The structure is defined by an α-helix that spans between Ile6-Ala26, and a cyclic disulphide bridged domain at the C-terminal end of the peptide sequence, between residues 23 and 29. A molecular dynamics simulation was employed to model the peptide's interactions with sodium dodecyl sulphate micelles, a widely used bacterial membrane-mimicking environment. Throughout the simulation, the peptide was found to maintain its α-helical conformation between residues Ile6-Ala26, while adopting a position parallel to the surface to micelle, which is energetically-favourable due to many hydrophobic and electrostatic contacts with the micelle.

scholarly journals Evolutionary conservation of the intrinsic disorder-based Radical-Induced Cell Death1 hub interactome

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Lise Friis Christensen ◽  
Lasse Staby ◽  
Katrine Bugge ◽  
Charlotte O’Shea ◽  
Birthe B. Kragelund ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Stress Responses ◽  
Plant Stress ◽  
Three Dimensional ◽  
Intrinsic Disorder ◽  
Dimensional Structure ◽  
Linear Motif ◽  
Intrinsically Disordered ◽  
Helix Formation ◽  
Α Helix

AbstractRadical-Induced Cell Death1 (RCD1) functions as a cellular hub interacting with intrinsically disordered transcription factor regions, which lack a well-defined three-dimensional structure, to regulate plant stress. Here, we address the molecular evolution of the RCD1-interactome. Using bioinformatics, its history was traced back more than 480 million years to the emergence of land plants with the RCD1-binding short linear motif (SLiM) identified from mosses to flowering plants. SLiM variants were biophysically verified to be functional and to depend on the same RCD1 residues as the DREB2A transcription factor. Based on this, numerous additional members may be assigned to the RCD1-interactome. Conservation was further strengthened by similar intrinsic disorder profiles of the transcription factor homologs. The unique structural plasticity of the RCD1-interactome, with RCD1-binding induced α-helix formation in DREB2A, but not detectable in ANAC046 or ANAC013, is apparently conserved. Thermodynamic analysis also indicated conservation with interchangeability between Arabidopsis and soybean RCD1 and DREB2A, although with fine-tuned co-evolved binding interfaces. Interruption of conservation was observed, as moss DREB2 lacked the SLiM, likely reflecting differences in plant stress responses. This whole-interactome study uncovers principles of the evolution of SLiM:hub-interactions, such as conservation of α-helix propensities, which may be paradigmatic for disorder-based interactomes in eukaryotes.

Structure and conformation of the hydrochloride of pseudoisocytidine, an antileukemic C-nucleoside

1980 ◽  
Vol 58 (16) ◽  
pp. 1633-1638 ◽  
Author(s):  
George I. Birnabaum ◽  
Kyoichi A. Watanabe ◽  
Jack J. Fox
Keyword(s):  
Heavy Atom ◽  
Three Dimensional ◽  
Direct Methods ◽  
Dimensional Structure ◽  
Side Chain ◽  
Hydrogen Atoms ◽  
Triclinic Space Group ◽  
X Ray Crystallography ◽  
Cell Dimensions ◽  
Sugar Ring

The three-dimensional structure of pseudoisocytidine hydrochloride was determined by X-ray crystallography. The crystals belong to the triclinic space group P1 and the cell dimensions are a = 6.623(2), b = 8.053(2), c = 6.201(2) Å, α = 108.35(2), β = 101.36(2), γ = 93.54(2) °. Intensity data were measured with a diffractometer and the structure was solved by a combination of heavy-atom and direct methods. Least-squares refinement, which included hydrogen atoms, converged at R = 0.040. The conformation about the glycosyl bond is anti (χCC = 21.6°), the pucker of the furanose ring is C(1′)exo, and the conformation of the —CH2OH side chain is gauche–trans (t). An examination of bond lengths indicates that of the three main resonance forms of the isocytosine cation the fully conjugated one contributes more to the structure than the cross-conjugated one. Bond angles in the sugar ring reflect its rare conformation.

scholarly journals Ribokinase fromLeishmania donovani: purification, characterization and X-ray crystallographic analysis

2018 ◽  
Vol 74 (2) ◽  
pp. 99-104 ◽  
Author(s):  
Santhosh Gatreddi ◽  
Sayanna Are ◽  
Insaf Ahmed Qureshi
Keyword(s):  
Functional Characterization ◽  
Three Dimensional ◽  
Protozoan Parasite ◽  
Crystallographic Analysis ◽  
Size Exclusion ◽  
Dimensional Structure ◽  
Diffusion Method ◽  
Gene Encoding ◽  
Cell Parameters ◽  
Α Helix

Leishmaniais an auxotrophic protozoan parasite which acquires D-ribose by transporting it from the host cell and also by the hydrolysis of nucleosides. The enzyme ribokinase (RK) catalyzes the first step of ribose metabolism by phosphorylating D-ribose using ATP to produce D-ribose-5-phosphate. To understand its structure and function, the gene encoding RK fromL. donovaniwas cloned, expressed and purified using affinity and size-exclusion chromatography. Circular-dichroism spectroscopy of the purified protein showed comparatively more α-helix in the secondary-structure content, and thermal unfolding revealed theTmto be 317.2 K. Kinetic parameters were obtained by functional characterization ofL. donovaniRK, and theKmvalues for ribose and ATP were found to be 296 ± 36 and 116 ± 9.0 µM, respectively. Crystals obtained by the hanging-drop vapour-diffusion method diffracted to 1.95 Å resolution and belonged to the hexagonal space groupP61, with unit-cell parametersa=b= 100.25,c= 126.77 Å. Analysis of the crystal content indicated the presence of two protomers in the asymmetric unit, with a Matthews coefficient (VM) of 2.45 Å3 Da−1and 49.8% solvent content. Further study revealed that human counterpart of this protein could be used as a template to determine the first three-dimensional structure of the RK from trypanosomatid parasites.

Thyroid Hormone Stereochemistry. II. Molecular Structure of Thyronine HCl Ethyl Ester Monohydrate

1974 ◽  
Vol 52 (17) ◽  
pp. 3042-3047 ◽  
Author(s):  
Arthur Camerman ◽  
Norman Camerman
Keyword(s):  
Ethyl Ester ◽  
Three Dimensional ◽  
Chloride Ion ◽  
Dimensional Structure ◽  
Side Chain ◽  
Monoclinic Space Group ◽  
X Ray Diffraction ◽  
Ether Linkage ◽  
Cell Dimensions ◽  
Phenyl Rings

The three-dimensional structure of L-thyronine, the non-iodinated physiologically inactive analog of thyroxine, has been determined by single crystal X-ray diffraction and compared to the active thyroid hormones. The compound crystallized as the monohydrate of thyronine hydrochloride ethyl ester in the monoclinic space group P21 with cell dimensions a = 10.502, b = 5.165, c = 17.940 Å, β = 109.74°. The structure was solved by Patterson methods to find the chloride ion and iterative Fourier maps to locate the rest of the atoms. Refinement was by anisotropic full-matrix least squares to convergence at R = 0.048.The two phenyl rings adopt a twisted orientation with respect to each other with angles of −37° and −67° between the plane of the inter-ring ether linkage and the planes of the α- and β-rings, respectively. This orientation differs considerably from that found in the iodinated thyronines. The conformation of the alanine side chain is remarkably similar to that of the alanine in the iodinated thyronines.

scholarly journals Insights into the molecular basis of sperm–egg recognition in mammals

Reproduction ◽  
2004 ◽  
Vol 127 (4) ◽  
pp. 417-422 ◽  
Author(s):  
Tanya Hoodbhoy ◽  
Jurrien Dean
Keyword(s):  
Zona Pellucida ◽  
Three Dimensional ◽  
Explanatory Models ◽  
Dimensional Structure ◽  
Side Chain ◽  
Egg Recognition ◽  
Three Dimensional Structure ◽  
Sperm Binding ◽  
Single Protein

The zona pellucida surrounding the egg and pre-implantation embryo is required for in vivo fertility and early development. Explanatory models of sperm–egg recognition need to take into account the ability of sperm to bind to ovulated eggs, but not to two-cell embryos. For the last two decades, investigators have sought to identify an individual protein or carbohydrate side chain as the ‘sperm receptor’. However, recent genetic data in mice are more consistent with the three-dimensional structure of the zona pellucida, rather than a single protein (or carbohydrate), determining sperm binding. The mouse and human zonae pellucidae contain three glycoproteins (ZP1, ZP2, ZP3) and, following fertilization, ZP2 is proteolytically cleaved. The replacement of endogenous mouse proteins with human ZP2, ZP3 or both does not alter taxon specificity of sperm binding or prevent fertility. Surprisingly, human ZP2 is not cleaved following fertilization and intact ZP2 correlates with persistent sperm binding to two-cell embryos. Taken together, these data support a model in which the cleavage status of ZP2 modulates the three-dimensional structure of the zona pellucida and determines whether sperm bind (uncleaved) or do not (cleaved).

Structure and conformation of the anticodon nucleoside 5-methoxyuridine in the solid state and in solution

1983 ◽  
Vol 61 (10) ◽  
pp. 2299-2304 ◽  
Author(s):  
George I. Birnbaum ◽  
Wayne J. P. Blonski ◽  
Frank E. Hruska
Keyword(s):  
Solid State ◽  
Three Dimensional ◽  
Direct Methods ◽  
Pyrimidine Ring ◽  
Dimensional Structure ◽  
Side Chain ◽  
Monoclinic Space Group ◽  
Hydrogen Atoms ◽  
Cell Dimensions ◽  
Enol Tautomer

The three-dimensional structure of 5-methoxyuridine (mo5U) was determined with much higher precision than in a previous study (Hillen etal. J. Carbohydr. Nucleosides Nucleotides, 5, 23 (1978)). The crystals belong to the monoclinic space group P21 and the cell dimensions are a = 8.916(2), b = 14.372(2), c = 4.714(1) Å, β = 97.44(2)°. Intensity data were measured with a diffractometer and the structure was solved by direct methods. Least-squares refinement, which included all hydrogen atoms, converged at R = 0.031. The conformation about the glycosyl bond is anti (χCN = 23.1°), the pucker of the ribose ring is C(3′)endo, and the conformation of the —CH2OH side chain is gauche+. A comparison of the bond lengths N(3)—C(4) and C(4)—O(4) with those in uridine does not support the conclusion of Hillen etal. about a shift to the enol tautomer in mo5U. However, there are other changes in the geometry of the pyrimidine ring due to substitution at C(5). A conformational analysis, based on 1H and 13C nmr data, shows that the preferred conformation in solution is that observed in the solid state.

scholarly journals Solution structure of the strawberry allergen Fra a 1

2012 ◽  
Vol 32 (6) ◽  
pp. 567-575 ◽  
Author(s):  
Christian Seutter von Loetzen ◽  
Kristian Schweimer ◽  
Wilfried Schwab ◽  
Paul Rösch ◽  
Olivia Hartl-Spiegelhauer
Keyword(s):  
Solution Structure ◽  
Three Dimensional ◽  
Protein Family ◽  
Dimensional Structure ◽  
Hydrophobic Pocket ◽  
Pigment Synthesis ◽  
Family Protein ◽  
Pr10 Protein ◽  
Α Helix

The PR10 family protein Fra a 1E from strawberry (Fragaria x ananassa) is down-regulated in white strawberry mutants, and transient RNAi (RNA interference)-mediated silencing experiments confirmed that Fra a 1 is involved in fruit pigment synthesis. In the present study, we determined the solution structure of Fra a 1E. The protein fold is identical with that of other members of the PR10 protein family and consists of a seven-stranded antiparallel β-sheet, two short V-shaped α-helices and a long C-terminal α-helix that encompass a hydrophobic pocket. Whereas Fra a 1E contains the glycine-rich loop that is highly conserved throughout the protein family, the volume of the hydrophobic pocket and the size of its entrance are much larger than expected. The three-dimensional structure may shed some light on its physiological function and may help to further understand the role of PR10 proteins in plants.

scholarly journals Characterization of the structure and redox behaviour of cytochrome c3 from Desulfovibrio baculatus by 1H-nuclear-magnetic-resonance spectroscopy

1993 ◽  
Vol 294 (3) ◽  
pp. 899-908 ◽  
Author(s):  
I B Coutinho ◽  
D L Turner ◽  
J LeGall ◽  
A V Xavier
Keyword(s):  
Chemical Shifts ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Resonance Spectroscopy ◽  
Cytochrome C3 ◽  
X Ray ◽  
1H Nuclear Magnetic Resonance ◽  
Proton Resonances ◽  
Nuclear Overhauser

Complete assignment of the aromatic and haem proton resonances in the cytochromes c3 isolated from Desulfovibrio baculatus strains (Norway 4, DSM 1741) and (DSM 1743) was achieved using one- and two-dimensional 1H n.m.r. Nuclear Overhauser enhancements observed between haem and aromatic resonances and between resonances due to different haems, together with the ring-current contributions to the chemical shifts of haem resonances, support the argument that the haem core architecture is conserved in the various cytochromes c3, and that the X-ray structure of the D. baculatus cytochrome c3 is erroneous. The relative orientation of the haems for both cytochromes was determined directly from n.m.r. data. The n.m.r. structures have a resolution of approximately 0.25 nm and are found to be in close agreement with the X-ray structure from D. vulgaris cytochrome c3. The proton assignments were used to relate the highest potential to a specific haem in the three-dimensional structure by monitoring the chemical-shift variation of several haem resonances throughout redox titrations followed by 1H n.m.r. The haem with highest redox potential is not the same as that in other cytochromes c3.

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