scholarly journals Structural Differences in KIR3DL1 and LILRB1 Interaction with HLA-B and the Loading Peptide Polymorphisms: In Silico Evidences

2015 ◽  
Vol 2015 ◽  
pp. 1-10
Author(s):  
Alba Grifoni ◽  
Atanas Patronov ◽  
Carla Montesano ◽  
Vittorio Colizzi ◽  
Massimo Amicosante
Keyword(s):  
Amino Acid ◽  
In Silico ◽  
Hla Class I ◽  
Class I ◽  
Amino Acid Residues ◽  
Strength Of Interaction ◽  
Structural Differences ◽  
Set Up

KIR3DL1 and LILRB1 interact with HLA class I. Using KIR3DL1/HLA-B interaction to set up the procedure, structural immune-informatics approaches have been performed in LILRB1/HLA-B alleles’ combination also considering the contribution of the HLA bound peptide. All KIR3DL1 alleles interact strongly with HLA-B alleles carrying Bw4 epitope and negative charged amino acid residues in peptide position P8 disrupt KIR3DL1 binding. HLA-B alleles carrying Ile 194 show a higher strength of interaction with LILRB1 in all the analyzed haplotypes. Finally, we hypothesize a contribution of the amino acid at position 1 of the HLA bound peptide in the modulation of HLA-B/LILRB1 interaction.

scholarly journals Predicting HLA Class I Non-Permissive Amino Acid Residues Substitutions

PLoS ONE ◽  
2012 ◽  
Vol 7 (8) ◽  
pp. e41710 ◽  
Author(s):  
T. Andrew Binkowski ◽  
Susana R. Marino ◽  
Andrzej Joachimiak
Keyword(s):  
Amino Acid ◽  
Hla Class I ◽  
Class I ◽  
Amino Acid Residues

scholarly journals Identification and in silico characterization of hemocyanin γ-type subunit protein in Vibrio harveyi infected freshwater prawn, Macrobrachium rosenbergii

2021 ◽  
Vol 42 (1) ◽  
pp. 14-23
Author(s):  
B.B. Patnaik ◽  
◽  
S. Baliarsingh ◽  
S. Sahoo ◽  
J.M. Chung ◽  
...  
Keyword(s):  
Amino Acid ◽  
In Silico ◽  
Vibrio Harveyi ◽  
Macrobrachium Rosenbergii ◽  
Full Length ◽  
Freshwater Prawn ◽  
Amino Acid Residues ◽  
Subunit Protein ◽  
In Silico Tools

Aim: Identification of full-length ORF of hemocyanin subunit-1 (Mr_HC_1) from the hepatopancreas transcriptome of freshwater prawn, Macrobrachium rosenbergii infected with Vibrio harveyi and characterization of its sequence and structure by in silico tools and softwares. Methodology: Illumina HiSeq and de novo assembled unigenes were scanned against PANM-DB to screen Mr_HC_1. FGENESH gene prediction and SMART programs were used to predict the ORF region. Subsequently, Clustal X2 and MEGA in-silico tools were used to understand the sequence relatedness and evolutionary status of Mr_HC_1. Structural prediction was performed by SWISS-MODEL and Ramachandran plot modeling programs Results: The full-length ORF was 1983 bp in length encoding a polypeptide of 661 amino acid residues. Mr_HC_1 showed a putative signal peptide of 21 amino acid residues at the N-terminus and three hemocyanin domains. Homology analysis of Mr_HC_1 amino acid sequence confirms maximum identity to M. nipponense hemocyanin subunit-1 (Mn_HC_1). Phylogenetic analysis showed that Mr_HC_1 is more closely related to the hemocyanin γ-type subunit of freshwater shrimps. Homology modeling of Mr_HC_1 showed homo-hexameric protein containing 12 copper ions. With a QMEAN score of -3.33 and model-template sequence identity of 59.15%, the predicted model of Mr_HC_1 is convincing Interpretation: This study characterizes the hemocyanin γ-type subunit protein of freshwater prawn, M. rosenbergii for future studies on host defense mechanisms.

scholarly journals In Silico Finding of Key Interaction Mediated α3β4 and α7 Nicotinic Acetylcholine Receptor Ligand Selectivity of Quinuclidine-Triazole Chemotype

2020 ◽  
Vol 21 (17) ◽  
pp. 6189
Author(s):  
Kuntarat Arunrungvichian ◽  
Sumet Chongruchiroj ◽  
Jiradanai Sarasamkan ◽  
Gerrit Schüürmann ◽  
Peter Brust ◽  
...  
Keyword(s):  
Amino Acid ◽  
Acetylcholine Receptor ◽  
Nicotinic Acetylcholine Receptor ◽  
In Silico ◽  
Amino Acid Residues ◽  
Nicotinic Acetylcholine ◽  
Selective Binding ◽  
Ligand Selectivity ◽  
Α7 Nachr ◽  
Nachr Subtype

The selective binding of six (S)-quinuclidine-triazoles and their (R)-enantiomers to nicotinic acetylcholine receptor (nAChR) subtypes α3β4 and α7, respectively, were analyzed by in silico docking to provide the insight into the molecular basis for the observed stereospecific subtype discrimination. Homology modeling followed by molecular docking and molecular dynamics (MD) simulations revealed that unique amino acid residues in the complementary subunits of the nAChR subtypes are involved in subtype-specific selectivity profiles. In the complementary β4-subunit of the α3β4 nAChR binding pocket, non-conserved AspB173 through a salt bridge was found to be the key determinant for the α3β4 selectivity of the quinuclidine-triazole chemotype, explaining the 47–327-fold affinity of the (S)-enantiomers as compared to their (R)-enantiomer counterparts. Regarding the α7 nAChR subtype, the amino acids promoting a however significantly lower preference for the (R)-enantiomers were the conserved TyrA93, TrpA149 and TrpB55 residues. The non-conserved amino acid residue in the complementary subunit of nAChR subtypes appeared to play a significant role for the nAChR subtype-selective binding, particularly at the heteropentameric subtype, whereas the conserved amino acid residues in both principal and complementary subunits are essential for ligand potency and efficacy.

scholarly journals The complex pattern of genetic associations of leprosy with HLA class I and class II alleles can be reduced to four amino acid positions

2020 ◽  
Vol 16 (8) ◽  
pp. e1008818
Author(s):  
Monica Dallmann-Sauer ◽  
Vinicius M. Fava ◽  
Chaïma Gzara ◽  
Marianna Orlova ◽  
Nguyen Van Thuc ◽  
...  
Keyword(s):  
Amino Acid ◽  
Hla Class I ◽  
Class Ii ◽  
Class I ◽  
Complex Pattern ◽  
Genetic Associations

scholarly journals A Mechanism for the Development of Chronic Traumatic Encephalopathy From Persistent Traumatic Brain Injury

2019 ◽  
Vol 13 ◽  
pp. 117906951984993 ◽  
Author(s):  
Melissa Demock ◽  
Steven Kornguth
Keyword(s):  
Traumatic Brain Injury ◽  
Amino Acid ◽  
Brain Injury ◽  
Tau Protein ◽  
Chronic Traumatic Encephalopathy ◽  
Hla Class I ◽  
Class I ◽  
Cross Linking ◽  
Neural Cells ◽  
The Cross

A mechanism that describes the progression of traumatic brain injury (TBI) to end-stage chronic traumatic encephalopathy (CTE) is offered in this article. This mechanism is based upon the observed increase in the concentration of both tau protein and of human leukocyte antigen (HLA) class I proteins; the HLA increase is expressed on the cell membrane of neural cells. These events follow the inflammatory responses caused by the repetitive TBI. Associated inflammatory changes include macrophage entry into the brain parenchyma from increased permeability of the blood-brain barrier (BBB) and microglial activation at the base of the sulci. The release of interferon gamma from the microglia and macrophages induces the marked increased expression of HLA class I proteins by the neural cells and subsequent redistribution of the tau proteins to the glial and neuronal surface. In those individuals with highly expressed HLA class I C, the high level of HLA binds tau protein electrostatically. The ionic region of HLA class I C (amino acid positions 50-90) binds to the oppositely charged ionic region of tau (amino acid positions 93-133). These interactions thereby shift the cellular localization of the tau and orient the tau spatially so that the cross-linking sites of tau (275-280 and 306-311) are aligned. This alignment facilitates the cross-linking of tau to form the intracellular and extracellular microfibrils of tau, the primary physiological characteristic of tauopathy. Following endocytosis of the membrane HLA/tau complex, these microfibrils accumulate and produce a tau-storage-like disease. Therefore, tauopathy is the secondary collateral process of brain injury, resulting from the substantial increase in tau and HLA expression on neural cells. This proposed mechanism suggests several potential targets for mitigating the clinical progression of TBI to CTE.

AB0009 The HLA Class I Region in Behçet's Disease: Identifying the Most Relevant Amino Acid Positions

2015 ◽  
Vol 74 (Suppl 2) ◽  
pp. 894.1-894
Author(s):  
L. Ortiz-Fernández ◽  
F.D. Carmona ◽  
M.-A. Montes-Cano ◽  
J.-R. García-Lozano ◽  
M. Conde-Jaldόn ◽  
...  
Keyword(s):  
Amino Acid ◽  
Behçet’S Disease ◽  
Behcet’S Disease ◽  
Behçet's Disease ◽  
Hla Class I ◽  
Class I ◽  
Behcet's Disease ◽  
Class I Region

scholarly journals Associations between HLA Class I Alleles and Escape Mutations in the Hepatitis B Virus Core Gene in New Zealand-Resident Tongans

2009 ◽  
Vol 84 (1) ◽  
pp. 621-629 ◽  
Author(s):  
William G. H. Abbott ◽  
Peter Tsai ◽  
Euphemia Leung ◽  
Alex Trevarton ◽  
Malakai Ofanoa ◽  
...  
Keyword(s):  
Amino Acid ◽  
Hepatitis B ◽  
Selection Pressure ◽  
Hla Class I ◽  
Core Gene ◽  
Class I ◽  
Positive Selection Pressure ◽  
Hla Class I Molecules ◽  
B Virus ◽  
Chronic Hbv

ABSTRACT The full repertoire of hepatitis B virus (HBV) peptides that bind to the common HLA class I molecules found in areas with a high prevalence of chronic HBV infection has not been determined. This information may be useful for designing immunotherapies for chronic hepatitis B. We identified amino acid residues under positive selection pressure in the HBV core gene by phylogenetic analysis of cloned DNA sequences obtained from HBV DNA extracted from the sera of Tongan subjects with inactive, HBeAg-negative chronic HBV infections. The repertoires of positively selected sites in groups of subjects who were homozygous for either HLA-B*4001 (n = 10) or HLA-B*5602 (n = 7) were compared. We identified 13 amino acid sites under positive selection pressure. A significant association between an HLA class I allele and the presence of nonsynonymous mutations was found at five of these sites. HLA-B*4001 was associated with mutations at E77 (P = 0.05) and E113 (P = 0.002), and HLA-B*5602 was associated with mutations at S21 (P = 0.02). In addition, amino acid mutations at V13 (P = 0.03) and E14 (P = 0.01) were more common in the seven subjects with an HLA-A*02 allele. In summary, we have developed an assay that can identify associations between HLA class I alleles and HBV core gene amino acids that mutate in response to selection pressure. This is consistent with published evidence that CD8+ T cells have a role in suppressing viral replication in inactive, HBeAg-negative chronic HBV infection. This assay may be useful for identifying the clinically significant HBV peptides that bind to common HLA class I molecules.

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