scholarly journals HLA-Modeler: Automated Homology Modeling of Human Leukocyte Antigens

2013 ◽  
Vol 2013 ◽  
pp. 1-6 ◽  
Author(s):  
Shinji Amari ◽  
Ryoichi Kataoka ◽  
Takashi Ikegami ◽  
Noriaki Hirayama
Keyword(s):  
Homology Modeling ◽  
Crystal Structures ◽  
Peptide Binding ◽  
Human Leukocyte ◽  
Antigenic Peptide ◽  
Structural Motif ◽  
3D Structures ◽  
Solvent Model ◽  
Hla Molecules ◽  
Homology Models

The three-dimensional (3D) structures of human leukocyte antigen (HLA) molecules are indispensable for the studies on the functions at molecular level. We have developed a homology modeling system named HLA-modeler specialized in the HLA molecules. Segment matching algorithm is employed for modeling and the optimization of the model is carried out by use of the PFROSST force field considering the implicit solvent model. In order to efficiently construct the homology models, HLA-modeler uses a local database of the 3D structures of HLA molecules. The structure of the antigenic peptide-binding site is important for the function and the 3D structure is highly conserved between various alleles. HLA-modeler optimizes the use of this structural motif. The leave-one-out cross-validation using the crystal structures of class I and class II HLA molecules has demonstrated that the rmsds of nonhydrogen atoms of the sites between homology models and crystal structures are less than 1.0 Å in most cases. The results have indicated that the 3D structures of the antigenic peptide-binding sites can be reproduced by HLA-modeler at the level almost corresponding to the crystal structures.

scholarly journals A Possible Molecular Mechanism of Immunomodulatory Activity of Bilirubin

2013 ◽  
Vol 2013 ◽  
pp. 1-4 ◽  
Author(s):  
Hideto Isogai ◽  
Noriaki Hirayama
Keyword(s):  
Autoimmune Diseases ◽  
Protective Factor ◽  
Peptide Binding ◽  
Antigenic Peptide ◽  
Antigenic Peptides ◽  
Discovery Research ◽  
Drug Discovery Research ◽  
Peptide Binding Groove ◽  
Binding Groove ◽  
Hla Molecules

Bilirubin is an endogenous product of heme degradation in mammals. Bilirubin has long been considered as a cytotoxic waste product that needs to be excreted. However, increasing evidence suggests that bilirubin possesses multiple biological activities. In particular, recent studies have shown that bilirubin should be a protective factor for several autoimmune diseases such as rheumatoid arthritis, multiple sclerosis, and systemic lupus erythematosus. Since these autoimmune diseases are closely associated with specific types of human leukocyte antigens (HLAs), we have hypothesized that bilirubin might bind to the antigenic peptide-binding groove of the HLA molecules and exert its immunosuppressive actions. In order to evaluate the hypothesis, theoretical docking studies between bilirubin and the relevant HLA molecules have been undertaken. The in silico studies have clearly shown that bilirubin may bind to the antigenic peptide-binding groove of the HLA molecules relevant to the autoimmune diseases with significant affinity. The bound bilirubin may block the binding of antigenic peptides to be presented to T cell receptors and lead to suppression of the autoimmune responses. Based on this hypothesis new drug discovery research for autoimmune diseases will be conducted.

scholarly journals Like wings of a bird: functional divergence and complementarity between HLA-A and HLA-B molecules

2020 ◽  
Author(s):  
Da Di ◽  
Jose Manuel Nunes ◽  
Wei Jiang ◽  
Alicia Sanchez-Mazas
Keyword(s):  
Balancing Selection ◽  
Functional Divergence ◽  
Peptide Binding ◽  
Human Leukocyte ◽  
Environmental Pressures ◽  
Protein Levels ◽  
Functional Complementarity ◽  
Vital Functions ◽  
Almost All ◽  
Immune Potential

Abstract Human leukocyte antigen (HLA) genes are among the most polymorphic of our genome, as a likely consequence of balancing selection related to their central role in adaptive immunity. HLA-A and HLA-B genes were recently suggested to evolve through a model of joint divergent asymmetric selection conferring all populations, including those with severe loss of diversity, an equivalent immune potential. However, the mechanisms by which these two genes might undergo joint evolution while displaying very distinct allelic profiles in populations worldwide are still unknown. To address this issue, we carried out extensive data analyses (among which factorial correspondence and linear modelling) on 2,909 common and rare HLA-A, HLA-B and HLA-C alleles and 200,000 simulated pathogenic peptides by taking into account sequence variation, predicted peptide-binding affinity and HLA allele frequencies in 123 populations worldwide. Our results show that HLA-A and HLA-B (but not HLA-C) molecules maintain considerable functional divergence in almost all populations, which likely plays an instrumental role in their immune defence. We also provide robust evidence of functional complementarity between HLA-A and HLA-B molecules, which display asymmetric relationships in terms of amino acid diversity at both inter- and intra-protein levels and in terms of promiscuous or fastidious peptide-binding specificities. Like two wings of a flying bird, the functional complementarity of HLA-A and HLA-B is a perfect example, in our genome, of duplicated genes sharing their capacity of assuming common vital functions while being submitted to complex and sometimes distinct environmental pressures.

scholarly journals Structural plasticity of KIR2DL2 and KIR2DL3 enables altered docking geometries atop HLA-C

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Shoeib Moradi ◽  
Sanda Stankovic ◽  
Geraldine M. O’Connor ◽  
Phillip Pymm ◽  
Bruce J. MacLachlan ◽  
...  
Keyword(s):  
Natural Killer Cells ◽  
Human Leukocyte Antigen ◽  
Nk Cells ◽  
Natural Killer ◽  
Crystal Structures ◽  
Killer Cell ◽  
Human Leukocyte ◽  
Leukocyte Antigen ◽  
Functional Differences ◽  
Molecular Bases

AbstractThe closely related inhibitory killer-cell immunoglobulin-like receptors (KIR), KIR2DL2 and KIR2DL3, regulate the activation of natural killer cells (NK) by interacting with the human leukocyte antigen-C1 (HLA-C1) group of molecules. KIR2DL2, KIR2DL3 and HLA-C1 are highly polymorphic, with this variation being associated with differences in the onset and progression of some human diseases. However, the molecular bases underlying these associations remain unresolved. Here, we determined the crystal structures of KIR2DL2 and KIR2DL3 in complex with HLA-C*07:02 presenting a self-epitope. KIR2DL2 differed from KIR2DL3 in docking modality over HLA-C*07:02 that correlates with variabilty of recognition of HLA-C1 allotypes. Mutagenesis assays indicated differences in the mechanism of HLA-C1 allotype recognition by KIR2DL2 and KIR2DL3. Similarly, HLA-C1 allotypes differed markedly in their capacity to inhibit activation of primary NK cells. These functional differences derive, in part, from KIR2DS2 suggesting KIR2DL2 and KIR2DL3 binding geometries combine with other factors to distinguish HLA-C1 functional recognition.

scholarly journals The molecular basis of how buried human leukocyte antigen polymorphism modulates natural killer cell function

2020 ◽  
Vol 117 (21) ◽  
pp. 11636-11647 ◽  
Author(s):  
Philippa M. Saunders ◽  
Bruce J. MacLachlan ◽  
Phillip Pymm ◽  
Patricia T. Illing ◽  
Yuanchen Deng ◽  
...  
Keyword(s):  
Human Leukocyte Antigen ◽  
Natural Killer ◽  
Nk Cell ◽  
Killer Cell ◽  
Peptide Binding ◽  
Human Leukocyte ◽  
Hla Class I ◽  
Cell Recognition ◽  
Leukocyte Antigen ◽  
Binding Cleft

Micropolymorphisms within human leukocyte antigen (HLA) class I molecules can change the architecture of the peptide-binding cleft, leading to differences in peptide presentation and T cell recognition. The impact of such HLA variation on natural killer (NK) cell recognition remains unclear. Given the differential association of HLA-B*57:01 and HLA-B*57:03 with the control of HIV, recognition of these HLA-B57 allomorphs by the killer cell immunoglobulin-like receptor (KIR) 3DL1 was compared. Despite differing by only two polymorphic residues, both buried within the peptide-binding cleft, HLA-B*57:01 more potently inhibited NK cell activation. Direct-binding studies showed KIR3DL1 to preferentially recognize HLA-B*57:01, particularly when presenting peptides with positively charged position (P)Ω-2 residues. In HLA-B*57:01, charged PΩ-2 residues were oriented toward the peptide-binding cleft and away from KIR3DL1. In HLA-B*57:03, the charged PΩ-2 residues protruded out from the cleft and directly impacted KIR3DL1 engagement. Accordingly, KIR3DL1 recognition of HLA class I ligands is modulated by both the peptide sequence and conformation, as determined by the HLA polymorphic framework, providing a rationale for understanding differences in clinical associations.

Comparison of homology models and crystal structures of cuticle‐degrading proteases from nematophagous fungi: structural basis of nematicidal activity

2011 ◽  
Vol 25 (6) ◽  
pp. 1894-1902 ◽  
Author(s):  
Lianming Liang ◽  
Shuqun Liu ◽  
Jinkui Yang ◽  
Zhaohui Meng ◽  
Liping Lei ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Nematophagous Fungi ◽  
Nematicidal Activity ◽  
Structural Basis ◽  
Homology Models

The Crystal Structures of the SH2 Domain of p56lckComplexed with Two Phosphonopeptides Suggest a Gated Peptide Binding Site

1995 ◽  
Vol 246 (2) ◽  
pp. 344-355 ◽  
Author(s):  
Vincent Mikol ◽  
Götz Baumann ◽  
Thomas H. Keller ◽  
Ute Manning ◽  
Mauro G.M. Zurini
Keyword(s):  
Binding Site ◽  
Crystal Structures ◽  
Peptide Binding ◽  
Sh2 Domain ◽  
Peptide Binding Site

scholarly journals Decachlorocyclopentasilanes coordinated by pairs of chloride anions, with different cations, but the same solvent molecules

2017 ◽  
Vol 73 (12) ◽  
pp. 1903-1907 ◽  
Author(s):  
Maximilian Moxter ◽  
Julian Teichmann ◽  
Hans-Wolfram Lerner ◽  
Michael Bolte ◽  
Matthias Wagner
Keyword(s):  
Crystal Structures ◽  
General Position ◽  
Rotation Axis ◽  
Chloride Ion ◽  
The Other ◽  
Structural Motif ◽  
Solvent Molecules

We have determined the crystal structures of two decachlorocyclopentasilanes, namely bis(tetra-n-butylammonium) dichloride decachlorocyclopentasilane dichloromethane disolvate, 2C16H36N+·2Cl−·Si5Cl10·2CH2Cl2, (I), and bis(tetraethylammonium) dichloride decachlorocyclopentasilane dichloromethane disolvate, 2C8H20N+·2Cl−·Si5Cl10·2CH2Cl2, (II), both of which crystallize with discrete cations, anions, and solvent molecules. In (I), the complete decachlorocyclopentasilane ring is generated by a crystallographic twofold rotation axis. In (II), one cation is located on a general position and the other two are disordered about centres of inversion. These are the first structures featuring the structural motif of a five-membered cyclopentasilane ring coordinated from both sides by a chloride ion. The extended structures of (I) and (II) feature numerous C—H...Cl interactions. In (II), the N atoms are located on centres of inversion and as a result, the ethylene chains are disordered over equally occupied orientations.

scholarly journals Preimplantation Factor (PIF) Promotes HLA-G, -E, -F, -C Expression in JEG-3 Choriocarcinoma Cells and Endogenous Progesterone Activity

2017 ◽  
Vol 43 (6) ◽  
pp. 2277-2296 ◽  
Author(s):  
Miya Soukaina Hakam ◽  
Jose Maria Miranda-Sayago ◽  
Soren Hayrabedyan ◽  
Krassimira Todorova ◽  
Patrick Simon Spencer ◽  
...  
Keyword(s):  
Protein Misfolding ◽  
Embryo Implantation ◽  
Human Leukocyte ◽  
Proteome Analysis ◽  
Bioinformatic Analysis ◽  
Receptor Protein ◽  
Trophoblast Invasion ◽  
Dependent Manner ◽  
Choriocarcinoma Cells ◽  
Hla Molecules

Background/Aims: Pregnancy success requires mandatory maternal tolerance of the semi/ allogeneic embryo involving embryo-derived signals. Expression levels of PreImplantation Factor (PIF), a novel peptide secreted by viable embryos, correlate with embryo development, and its early detection in circulation correlates with a favourable pregnancy outcome. PIF enhances endometrial receptivity to promote embryo implantation. Via the p53 pathway, it increases trophoblast invasion, improving cell survival / immune privilege. PIF also reduces spontaneous and LPS-induced foetal death in immune naïve murine model. We examined PIF effect on gene expression of human leukocyte antigen (HLA-G, -E -F and –C) and the influence of PIF on local progesterone activity in JEG-3 choriocarcinoma cells. Methods: PIF and progesterone (P4) effects on JEG-3 cells surface and intracellular HLA molecules was tested using monoclonal antibodies, flow cytometry, and Western blotting. PIF and IL17 effects on P4 and cytokines secretion was determined by ELISA. PIF and P4 effects on JEG-3 cells proteome was examined using 2D gel staining followed by spot analysis, mass spectrometry and bioinformatic analysis. Results: In cytotrophoblastic JEG-3 cells PIF increased intracellular expression of HLA-G, HLA-F, HLA-E and HLA-C and surface expression of HLA-G, HLA-E and HLA-C in dose and time dependent manner. In case of HLA-E, -F results were confirmed also by Western blot. Proteome analysis confirmed an increase in HLA-G, pro-tolerance FOXP3+ regulatory T cells (Tregs), coagulation factors and complement regulator. In contrast, PIF reduced PRDX2 and HSP70s to negate oxidative stress and protein misfolding. PIF enhanced local progesterone activity, increasing steroid secretion and the receptor protein. It also promoted the secretion of the Th1/Th2 cytokines (IL-10, IL-1β, IL-8, GM-CSF and TGF-β1), resulting in improved maternal signalling. Conclusion: PIF can generate a pro-tolerance milieu by enhancing the expression of HLA molecules and by amplifying endogenous progesterone activity. A Fast-Track clinical trial for autoimmune disease has been satisfactorily completed. The acquired data warrants PIF use for the treatment of early pregnancy disorders.

Peptide Binding in OppA, the Crystal Structures of the Periplasmic Oligopeptide Binding Protein in the Unliganded Form and in Complex with Lysyllysine†,‡

Biochemistry ◽  
1997 ◽  
Vol 36 (32) ◽  
pp. 9747-9758 ◽  
Author(s):  
Sara H. Sleigh ◽  
Jeremy R. H. Tame ◽  
Eleanor J. Dodson ◽  
Anthony J. Wilkinson
Keyword(s):  
Crystal Structures ◽  
Binding Protein ◽  
Peptide Binding
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