Two Polymorphisms Facilitate Differences in Plasticity between Two Chicken Major Histocompatibility Complex Class I Proteins
Publication Date
February 20, 2014
Journal
PLOS ONE
Authors
Alistair Bailey, Andy Van Hateren, Tim Elliott & Jörn M. Werner
Volume
9
Issue
2
Pages
e89657
DOI
https://dx.plos.org/10.1371/journal.pone.0089657
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0089657
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/24586943
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3930747
Europe PMC
http://europepmc.org/abstract/MED/24586943
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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1392373"], "description"=>"<p>For each 420ns molecular dynamics simulation of BF2*15∶01 and BF2*19∶01 PCA was performed using a common peptide free backbone structure. A) Contributions of the first 50 PCs to the total variance of the backbone atomic motions. B) Porcupine plots indicate the magnitude and direction of motion for each backbone atom along PC1 and 2 in both the peptide bound and peptide free states. The magnitude between extremes is indicated by the colour bar. C) Gibbs free energy landscapes are generated from the principal coordinates of PC1 and PC2 and transformed by treatment as a Boltzmann ensemble. Individual probability densities for PC1 and PC2 are plotted on the outside adjacent axes.</p>", "links"=>[], "tags"=>["Biochemistry", "proteins", "protein structure", "Computational biology", "population genetics", "Genetic polymorphism", "Sequence analysis", "immunology", "Antigen processing and recognition", "Major histocompatibility complex", "computational chemistry", "molecular dynamics", "mhc"], "article_id"=>939630, "categories"=>["Biological Sciences", "Chemistry"], "users"=>["Alistair Bailey", "Andy van Hateren", "Tim Elliott", "Jörn M. Werner"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0089657.g003", "stats"=>{"downloads"=>0, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_global_dynamics_of_MHC_I_identified_by_Principal_Component_Analysis_/939630", "title"=>"The global dynamics of MHC I identified by Principal Component Analysis.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-02-20 02:55:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/1392388", "https://ndownloader.figshare.com/files/1392389", "https://ndownloader.figshare.com/files/1392390", "https://ndownloader.figshare.com/files/1392391", "https://ndownloader.figshare.com/files/1392392", "https://ndownloader.figshare.com/files/1392393", "https://ndownloader.figshare.com/files/1392394"], "description"=>"<div><p>Major histocompatibility complex class I molecules (MHC I) present peptides to cytotoxic T-cells at the surface of almost all nucleated cells. The function of MHC I molecules is to select high affinity peptides from a large intracellular pool and they are assisted in this process by co-factor molecules, notably tapasin. In contrast to mammals, MHC homozygous chickens express a single MHC I gene locus, termed BF2, which is hypothesised to have co-evolved with the highly polymorphic tapasin within stable haplotypes. The BF2 molecules of the B15 and B19 haplotypes have recently been shown to differ in their interactions with tapasin and in their peptide selection properties. This study investigated whether these observations might be explained by differences in the protein plasticity that is encoded into the MHC I structure by primary sequence polymorphisms. Furthermore, we aimed to demonstrate the utility of a complimentary modelling approach to the understanding of complex experimental data. Combining mechanistic molecular dynamics simulations and the primary sequence based technique of statistical coupling analysis, we show how two of the eight polymorphisms between BF2*15∶01 and BF2*19∶01 facilitate differences in plasticity. We show that BF2*15∶01 is intrinsically more plastic than BF2*19∶01, exploring more conformations in the absence of peptide. We identify a protein sector of contiguous residues connecting the membrane bound α<sub>3</sub> domain and the heavy chain peptide binding site. This sector contains two of the eight polymorphic residues. One is residue 22 in the peptide binding domain and the other 220 is in the α<sub>3</sub> domain, a putative tapasin binding site. These observations are in correspondence with the experimentally observed functional differences of these molecules and suggest a mechanism for how modulation of MHC I plasticity by tapasin catalyses peptide selection allosterically.</p></div>", "links"=>[], "tags"=>["Biochemistry", "proteins", "protein structure", "Computational biology", "population genetics", "Genetic polymorphism", "Sequence analysis", "immunology", "Antigen processing and recognition", "Major histocompatibility complex", "computational chemistry", "molecular dynamics", "polymorphisms", "differences", "plasticity", "histocompatibility"], "article_id"=>939643, "categories"=>["Biological Sciences", "Chemistry"], "users"=>["Alistair Bailey", "Andy van Hateren", "Tim Elliott", "Jörn M. Werner"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0089657.s001", "https://dx.doi.org/10.1371/journal.pone.0089657.s002", "https://dx.doi.org/10.1371/journal.pone.0089657.s003", "https://dx.doi.org/10.1371/journal.pone.0089657.s004", "https://dx.doi.org/10.1371/journal.pone.0089657.s005", "https://dx.doi.org/10.1371/journal.pone.0089657.s006", "https://dx.doi.org/10.1371/journal.pone.0089657.s007"], "stats"=>{"downloads"=>9, "page_views"=>57, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Two_Polymorphisms_Facilitate_Differences_in_Plasticity_between_Two_Chicken_Major_Histocompatibility_Complex_Class_I_Proteins_/939643", "title"=>"Two Polymorphisms Facilitate Differences in Plasticity between Two Chicken Major Histocompatibility Complex Class I Proteins", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-02-20 02:55:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/1392376"], "description"=>"<p>Statistical coupling analysis (SCA) was carried out on a multiple sequence alignment (MSA) of 141 sequences obtained from a similarity search querying the BF2*15∶01 heavy chain as described in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0089657#pone.0089657-Smock1\" target=\"_blank\">[30]</a>. A) The degree of conservation of each heavy chain residue i in the MSA is computed as the Kullback-Leibler relative entropy D<sub>i</sub>. Bigger bars indicate greater conservation. The 85 protein sector residues are in red, 6 polymorphic residues between BF2*15∶01 and BF2*19∶01 are in green and the 2 residues that are both polymorphic and part of the protein sector are in blue. All other residues are in grey. B) Protein sector residues are mapped as spheres onto a ribbon representation of the BF2*15∶01 structure. Colours as (A), with the peptide as yellow sticks. C) and D) Space filling representations of the MHC I heavy chain, coloured as (B). The contiguous network of residues forming a protein sector comprises of 31% of heavy chain residues.</p>", "links"=>[], "tags"=>["Biochemistry", "proteins", "protein structure", "Computational biology", "population genetics", "Genetic polymorphism", "Sequence analysis", "immunology", "Antigen processing and recognition", "Major histocompatibility complex", "computational chemistry", "molecular dynamics", "mhc"], "article_id"=>939633, "categories"=>["Biological Sciences", "Chemistry"], "users"=>["Alistair Bailey", "Andy van Hateren", "Tim Elliott", "Jörn M. Werner"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0089657.g004", "stats"=>{"downloads"=>1, "page_views"=>20, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Identification_of_a_protein_sector_in_chicken_MHC_I_/939633", "title"=>"Identification of a protein sector in chicken MHC I.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-02-20 02:55:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/1392369"], "description"=>"<p>A) and C) The standard deviation of the internal angle of rotation φ measuring the rotation around N-Cα bond of each residue of BF2*15∶01 and BF2*19∶01 from 420ns of molecular dynamics simulation in the peptide bound and peptide free states. Peptide bound measurements are shown as black bars and peptide free as red bars. B) and D) Ribbon representations of BF2*15∶01 and BF2*19∶01 with the peptide free simulations φ angle standard deviations mapped as increasing from blue to white to red, with annotations on the BF2*15∶01 heavy chain. Glycine residues are coloured black.</p>", "links"=>[], "tags"=>["Biochemistry", "proteins", "protein structure", "Computational biology", "population genetics", "Genetic polymorphism", "Sequence analysis", "immunology", "Antigen processing and recognition", "Major histocompatibility complex", "computational chemistry", "molecular dynamics", "mhc", "conformational"], "article_id"=>939626, "categories"=>["Biological Sciences", "Chemistry"], "users"=>["Alistair Bailey", "Andy van Hateren", "Tim Elliott", "Jörn M. Werner"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0089657.g002", "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Quantification_of_the_flexibility_of_MHC_I_by_conformational_966_angle_standard_deviation_/939626", "title"=>"Quantification of the flexibility of MHC I by conformational φ angle standard deviation.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-02-20 02:55:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/1392366"], "description"=>"<p>A) The structure of the lumenal domain of a chicken MHC Class I molecule. A space filling representation of the heavy chain is shown, formed of α<sub>1</sub>– α<sub>2</sub> peptide binding domain and the membrane proximal α<sub>3</sub> domain, creating a complex with a non-covalently bound β<sub>2</sub>m light chain shown as a ribbon representation. B) The peptide is shown as a stick representation in grey, non-covalently bound into the groove formed between the α<sub>1</sub> and α<sub>2</sub> helices. The sites of the polymorphic residues between BF2*15∶01 and BF2*19∶01 indicated in green, with the location of residue 22 indicated in the peptide binding domain below the α<sub>1</sub> helix.</p>", "links"=>[], "tags"=>["Biochemistry", "proteins", "protein structure", "Computational biology", "population genetics", "Genetic polymorphism", "Sequence analysis", "immunology", "Antigen processing and recognition", "Major histocompatibility complex", "computational chemistry", "molecular dynamics", "polymorphisms", "mhc", "alleles"], "article_id"=>939623, "categories"=>["Biological Sciences", "Chemistry"], "users"=>["Alistair Bailey", "Andy van Hateren", "Tim Elliott", "Jörn M. Werner"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0089657.g001", "stats"=>{"downloads"=>1, "page_views"=>67, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_structure_and_polymorphisms_of_chicken_MHC_Class_I_alleles_BF2_15_8758_01_and_BF2_19_8758_01_/939623", "title"=>"The structure and polymorphisms of chicken MHC Class I alleles BF2*15∶01 and BF2*19∶01.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-02-20 02:55:56"}

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