scholarly journals Main Chain Hydrogen Bond Interactions in the Binding of Proline-rich Gluten Peptides to the Celiac Disease-associated HLA-DQ2 Molecule

2005 ◽  
Vol 280 (23) ◽  
pp. 21791-21796 ◽  
Author(s):  
Elin Bergseng ◽  
Jiang Xia ◽  
Chu-Young Kim ◽  
Chaitan Khosla ◽  
Ludvig M. Sollid
Keyword(s):  
Hydrogen Bond ◽  
Major Histocompatibility Complex ◽  
Celiac Disease ◽  
Hydrogen Bonds ◽  
Main Chain ◽  
Amide Hydrogen ◽  
Hydrogen Bond Interactions ◽  
Histocompatibility Complex ◽  
Gluten Peptides ◽  
Hla Dq2

Binding of peptide epitopes to major histocompatibility complex proteins involves multiple hydrogen bond interactions between the peptide main chain and major histocompatibility complex residues. The crystal structure of HLA-DQ2 complexed with the αI-gliadin epitope (LQPFPQPELPY) revealed four hydrogen bonds between DQ2 and peptide main chain amides. This is remarkable, given that four of the nine core residues in this peptide are proline residues that cannot engage in amide hydrogen bonding. Preserving main chain hydrogen bond interactions despite the presence of multiple proline residues in gluten peptides is a key element for the HLA-DQ2 association of celiac disease. We have investigated the relative contribution of each main chain hydrogen bond interaction by preparing a series of N-methylated αI epitope analogues and measuring their binding affinity and off-rate constants to DQ2. Additionally, we measured the binding of αI-gliadin peptide analogues in which norvaline, which contains a backbone amide hydrogen bond donor, was substituted for each proline. Our results demonstrate that hydrogen bonds at P4 and P2 positions are most important for binding, whereas the hydrogen bonds at P9 and P6 make smaller contributions to the overall binding affinity. There is no evidence for a hydrogen bond between DQ2 and the P1 amide nitrogen in peptides without proline at this position. This is a unique feature of DQ2 and is likely a key parameter for preferential binding of proline-rich gluten peptides and development of celiac disease.

scholarly journals Crystal structure of 4-{[(1H-1,2,4-triazol-1-yl)methyl]sulfanyl}phenol

2014 ◽  
Vol 70 (10) ◽  
pp. o1106-o1106
Author(s):  
Yong-Le Zhang ◽  
Chuang Zhang ◽  
Wei Guo ◽  
Jing Wang
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Benzene Ring ◽  
Title Compound ◽  
Three Dimensional ◽  
Triazole Ring ◽  
Hydrogen Bond Interactions ◽  
Compound C ◽  
Dimensional Network

In the title compound, C9H9N3OS, the plane of the benzene ring forms a dihedral angle of 33.40 (5)° with that of the triazole group. In the crystal, molecules are linked by O—H...N hydrogen bonds involving the phenol –OH group and one of the unsubstituted N atoms of the triazole ring, resulting in chains along [010]. These chains are further extended into a layer parallel to (001) by weak C—H...N hydrogen-bond interactions. Aromatic π–π stacking [centroid–centroid separation = 3.556 (1) Å] between the triazole rings links the layers into a three-dimensional network.

Formation and distortion of iodidoantimonates(III): the first isolated [SbI6]3−octahedron

2017 ◽  
Vol 73 (3) ◽  
pp. 432-442 ◽  
Author(s):  
Maciej Bujak
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Crystal Engineering ◽  
Structural Parameters ◽  
Hybrid Structure ◽  
Organic Hybrid ◽  
Hydrogen Bond Interactions ◽  
Different Types ◽  
Spatial Dimensions ◽  
Induced Changes

The ability to intentionally construct, through different types of interactions, inorganic–organic hybrid materials with desired properties is the main goal of inorganic crystal engineering. The primary deformation, related to intrinsic interactions within inorganic substructure, and the secondary deformation, mainly caused by the hydrogen bond interactions, are both responsible for polyhedral distortions of halogenidoantimonates(III) with organic cations. The evolution of structural parameters, in particular the Sb—I secondary- and O/N/C—H...I hydrogen bonds, as a function of temperature assists in understanding the contribution of those two distortion factors to the irregularity of [SbI6]3−polyhedra. In tris(piperazine-1,4-diium) bis[hexaiodidoantimonate(III)] pentahydrate, (C4H12N2)3[SbI6]2·5H2O (TPBHP), where the isolated [SbI6]3–units were found, distortion is governed only by O/N/C—H...I hydrogen bonds, whereas in piperazine-1,4-diium bis[tetraiodidoantimonate(III)] tetrahydrate, (C4H12N2)[SbI4]2·4H2O (PBTT), both primary and O—H...I secondary factors cause the deformation of one-dimensional [{SbI4}n]n−chains. The larger in spatial dimensions piperazine-1,4-diium cations, in contrast to the smaller water of crystallization molecules, do not significantly contribute to the octahedral distortion, especially in PBTT. The formation of isolated [SbI6]3−ions in TPBHP is the result of specific second coordination sphere hydrogen bond interactions that stabilize the hybrid structure and simultaneously effectively separate and prevent [SbI6]3−units from mutual interactions. The temperature-induced changes, further supported by the analysis of data retrieved from the Cambridge Structural Database, illustrate the significance of both primary and secondary distortion factors on the deformation of octahedra. Also, a comparison of packing features in the studied hybrids with those in the non-metal containing piperazine-1,4-diium diiodide diiodine (C4H12N2)I2·I2(PDD) confirms the importance and hierarchy of different types of interactions.

Comparison of the structure of (E)-2-(2-benzylidenehydrazinylidene)quinoxaline with those of its chloro- and bromobenzylidene analogues

2013 ◽  
Vol 69 (8) ◽  
pp. 920-926
Author(s):  
Ligia Rebelo Gomes ◽  
John Nicolson Low ◽  
Ana S. M. C. Rodrigues ◽  
James L. Wardell ◽  
Marcus V. N. de Souza ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Supramolecular Structures ◽  
Stacking Interactions ◽  
Asymmetric Unit ◽  
Hydrogen Bond Interactions ◽  
Π Stacking ◽  
Derivatives Of

(E)-2-(2-Benzylidenehydrazinylidene)quinoxaline, C15H12N4, crystallized with two molecules in the asymmetric unit. The structures of six halogen derivatives of this compound were also investigated: (E)-2-[2-(2-chlorobenzylidene)hydrazinylidene]quinoxaline, C15H11ClN4; (E)-2-[2-(3-chlorobenzylidene)hydrazinylidene]quinoxaline, C15H11ClN4; (E)-2-[2-(4-chlorobenzylidene)hydrazinylidene]quinoxaline, C15H11ClN4; (E)-2-[2-(2-bromobenzylidene)hydrazinylidene]quinoxaline, C15H11BrN4; (E)-2-[2-(3-bromobenzylidene)hydrazinylidene]quinoxaline, C15H11BrN4; (E)-2-[2-(4-bromobenzylidene)hydrazinylidene]quinoxaline, C15H11BrN4. The 3-Cl and 3-Br compounds are isomorphous, as are the 4-Cl and 4-Br compounds. In all of these compounds, it was found that the supramolecular structures are governed by similar predominant patterns,viz.strong intermolecular N—H...N(pyrazine) hydrogen bonds supplemented by weak C—H...N(pyrazine) hydrogen-bond interactions in the 2- and 3-halo compounds and by C—H...Cl/Br interactions in the 4-halo compounds. In all compounds, there are π–π stacking interactions.

scholarly journals Polymorphisms in pockets of major histocompatibility complex class I molecules influence peptide preference.

1993 ◽  
Vol 177 (6) ◽  
pp. 1713-1721 ◽  
Author(s):  
E M Rohren ◽  
L R Pease ◽  
H L Ploegh ◽  
T N Schumacher
Keyword(s):  
Major Histocompatibility Complex ◽  
Major Histocompatibility Complex Class ◽  
Main Chain ◽  
Cytotoxic T Cells ◽  
Peptide Libraries ◽  
Class I ◽  
Complex Class ◽  
Major Histocompatibility ◽  
Histocompatibility Complex ◽  
Static View

The set of peptides that is bound by a given major histocompatibility complex class I product can be described by one or two properly spaced anchor residues, and two properly spaced peptide termini, approximately 8-10 residues apart. Using radiolabeled peptide libraries, we examined whether mutations in those "pockets" in class I Kb molecules that do not seem critically involved in the interaction with the peptide anchor residues, do exert an effect on the set of preferred peptides. We find that mutations in all the pockets found in the structure of Kb have a significant effect on the peptide preference of the molecule, and their recognition by cytotoxic T cells. Alterations in substrate specificity are also observed for mutations involving residues that interact with main chain atoms in both peptide termini. These findings challenge a static view of the interaction of peptide termini with their respective pockets in the class I molecule, and imply a role for the minor pockets in peptide selectivity.

The conformational restriction of synthetic peptides, including a malaria peptide, for use as immunogens

1989 ◽  
Vol 323 (1217) ◽  
pp. 565-572 ◽  
Keyword(s):  
Hydrogen Bond ◽  
Plasmodium Falciparum ◽  
Amino Acid ◽  
Hydrogen Bonds ◽  
Synthetic Peptides ◽  
Synthetic Methods ◽  
Amide Hydrogen ◽  
Conformational Restriction ◽  
Conformationally Restricted ◽  
New Strategy

A new strategy is advanced for the conformational restriction of peptidyl immunogens. Our approach is to replace putative amide-amide hydrogen bonds with covalent hydrogen-bond mimics. Because on average every other amino acid in a protein engages in this bond, the syntheses of diversely shaped peptides can be contemplated. Synthetic methods for introducing a potential hydrogen-bond mimic into a peptide with α-helical potential is reported and the structural consequences are discussed. The replacement of the hydrogen bond with a chemical link will modify as well as shape the peptide. To explore the consequences of these changes, a potential synthetic vaccine for malaria, the repeating tetrapeptide Asn-Pro-Asn-Ala, was conformationally restricted. Antibodies to the shaped malarial peptide showed a strong cross reaction with Plasmodium falciparum sporozoites.

scholarly journals Interactions of Aggregating Peptides Probed by IR-UV Action Spectroscopy

2018 ◽  
Author(s):  
Sjors Bakels ◽  
E.M. Meijer ◽  
Mart Greuell ◽  
Sebastiaan Porskamp ◽  
George Rouwhorst ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Self Assembly ◽  
Intermolecular Hydrogen Bond ◽  
Beta Sheet ◽  
Dispersion Interactions ◽  
Intramolecular Hydrogen Bonds ◽  
Action Spectroscopy ◽  
Hydrogen Bond Interactions ◽  
Intramolecular Hydrogen

Peptide aggregation, the self-assembly of peptides into structured beta-sheet fibril structures, is driven by a combination of intra- and intermolecular interactions. Here, the interplay between intramolecular and formed inter-sheet hydrogen bonds and the effect of dispersion interactions on the formation of neutral, isolated, peptide dimers is studied by infrared action spectroscopy. Therefore, four different homo- and hetereogeneous dimers formed from three different alanine-based model peptides have been studied under controlled and isolated conditions. The peptides differ from one another in the presence and location of a UV chromophore containing cap on either the C- or N-terminus. Conformations of the monomers of the peptides direct the final dimer structure: strongly hydrogen bonded or folded structures result in weakly bound dimers. Here the intramolecular hydrogen bonds are favored over new intermolecular hydrogen bond interactions. In contrast, linearly folded monomers are the ideal template to form parallel beta-sheet type structures. The weak intramolecular hydrogen bonds present in the linear monomers are replaced by the stronger inter-sheet hydrogen bond interactions. The influence of π-π disperion interactions on the structure of the dimer is minimal, the phenyl rings have the tendency to fold away from the peptide backbone to favour intermolecular hydrogen bond interactions. Quantum chemical calculations confirm our experimental observations.

scholarly journals Isostructural Inorganic–Organic Piperazine-1,4-diium Chlorido- and Bromidoantimonate(III) Monohydrates: Octahedral Distortions and Hydrogen Bonds

Molecules ◽  
2020 ◽  
Vol 25 (6) ◽  
pp. 1361
Author(s):  
Maciej Bujak ◽  
Dawid Siodłak
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Ligand Exchange ◽  
Structural Parameters ◽  
Monoclinic Space Group ◽  
X Ray Diffraction ◽  
Hydrogen Bond Interactions ◽  
Hybrid Crystals ◽  
Structural Database ◽  
Hydrogen Bonded Systems

Halogenidoantimonate(III) monohydrates of the (C4H12N2)[SbX5]·H2O (X = Cl, 1 or Br, 2) formula, crystallizing in the same monoclinic space group of P21/n, are isostructural, with an isostructurality index close to 99%. The single crystal X-ray diffraction data do not show any indication of phase transition in cooling these crystals from room temperature to 85 K. Both hybrid crystals are built up from [SbX6]3– octahedra that are joined together by a common edge forming isolated bioctahedral [Sb2X10]4– units, piperazine-1,4-diium (C4H12N2)2+ cations and water of crystallization molecules. These structural components are joined together by related but somewhat different O/N/C–H···X and N–H···O hydrogen bonded systems. The evolution of structural parameters, notably the secondary Sb–X bonds along with the associated X/Sb–Sb/X–X/Sb angles and O/N/C–H···X hydrogen bonds, as a function of ligand exchange and temperature, along with their influence on the irregularity of [SbX6]3– octahedra, was determined. The comparison of packing features and hydrogen bond parameters, additionally supported by the Hirshfeld surface analysis and data retrieved from the Cambridge Structural Database, demonstrates the hierarchy and importance of hydrogen bond interactions that influence the irregularity of single [SbX6]3– units.

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