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Immunogenetics
2006 Jun 01;585-6:433-42. doi: 10.1007/s00251-006-0114-5.
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Polymorphism, natural selection, and structural modeling of class Ia MHC in the African clawed frog (Xenopus laevis).
Bos DH, Waldman B.
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In the African clawed frog (Xenopus laevis), two deeply divergent allelic lineages of multiple genes of the class I MHC region have been discovered. For the MHC class I UAA locus, functional differences and the molecular basis for lineages maintenance are unknown. Alleles of linked class I region genes also exhibit strong disequilibrium with specific MHC alleles, but the underlying cause is not clear. We use MHC class Ia sequence data to estimate substitution rates and investigate structural differences between allelic lineages from protein models. Results indicate the operation of natural selection, and differences in the steric properties in the F pocket of the peptide-binding region among lineages. Variability in this pocket likely enables allelic lineages to bind very different sets of peptides and to interact differently with MHC chaperones in the endoplasmic reticulum. These results constitute evidence of the molecular evolutionary basis for 1) the maintenance of allelic lineages, 2) functional differences among lineages, and 3) strong linkage disequilibrium of allelic variants of class I region genes in X. laevis.
Abascal,
ProtTest: selection of best-fit models of protein evolution.
2005, Pubmed
Abascal,
ProtTest: selection of best-fit models of protein evolution.
2005,
Pubmed Andolfatto,
The effect of gene conversion on intralocus associations.
1998,
Pubmed Anisimova,
Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites.
2003,
Pubmed Anisimova,
Accuracy and power of bayes prediction of amino acid sites under positive selection.
2002,
Pubmed Apanius,
The nature of selection on the major histocompatibility complex.
1997,
Pubmed Beissbarth,
Increased efficiency of folding and peptide loading of mutant MHC class I molecules.
2000,
Pubmed Berman,
The Protein Data Bank.
2000,
Pubmed Bos,
Using models of nucleotide evolution to build phylogenetic trees.
2005,
Pubmed Bos,
Evolution by recombination and transspecies polymorphism in the MHC class I gene of Xenopus laevis.
2006,
Pubmed
,
Xenbase Boyington,
Crystal structure of an NK cell immunoglobulin-like receptor in complex with its class I MHC ligand.
2000,
Pubmed Carrington,
The influence of HLA genotype on AIDS.
2003,
Pubmed Crandall,
Parallel evolution of drug resistance in HIV: failure of nonsynonymous/synonymous substitution rate ratio to detect selection.
1999,
Pubmed Doherty,
Enhanced immunological surveillance in mice heterozygous at the H-2 gene complex.
1975,
Pubmed Elliott,
The optimization of peptide cargo bound to MHC class I molecules by the peptide-loading complex.
2005,
Pubmed Ferrara,
Bone marrow transplantation from unrelated donors: the impact of mismatches with substitutions at position 116 of the human leukocyte antigen class I heavy chain.
2001,
Pubmed Flajnik,
Identification of class I major histocompatibility complex encoded molecules in the amphibian Xenopus.
1984,
Pubmed
,
Xenbase Flajnik,
Two ancient allelic lineages at the single classical class I locus in the Xenopus MHC.
1999,
Pubmed
,
Xenbase Gao,
Crystal structure of the complex between human CD8alpha(alpha) and HLA-A2.
1997,
Pubmed Garbi,
Accessory molecules in the assembly of major histocompatibility complex class I/peptide complexes: how essential are they for CD8(+) T-cell immune responses?
2005,
Pubmed Garboczi,
Structure of the complex between human T-cell receptor, viral peptide and HLA-A2.
1996,
Pubmed Grandea,
Tapasin: an ER chaperone that controls MHC class I assembly with peptide.
2001,
Pubmed Guex,
Protein modelling for all.
1999,
Pubmed Guex,
SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling.
1997,
Pubmed Guindon,
A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood.
2003,
Pubmed Harris,
Calreticulin and calnexin interact with different protein and glycan determinants during the assembly of MHC class I.
1998,
Pubmed Hashimoto,
Conservation and diversification of MHC class I and its related molecules in vertebrates.
1999,
Pubmed Hildebrand,
HLA class I polymorphism has a dual impact on ligand binding and chaperone interaction.
2002,
Pubmed Hughes,
Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection.
1988,
Pubmed Hülsmeyer,
HLA-B27 subtypes differentially associated with disease exhibit subtle structural alterations.
2002,
Pubmed Ina,
New methods for estimating the numbers of synonymous and nonsynonymous substitutions.
1995,
Pubmed Joly,
Co-evolution of rat TAP transporters and MHC class I RT1-A molecules.
1998,
Pubmed Jones,
The rapid generation of mutation data matrices from protein sequences.
1992,
Pubmed Kaufman,
Different features of the MHC class I heterodimer have evolved at different rates. Chicken B-F and beta 2-microglobulin sequences reveal invariant surface residues.
1992,
Pubmed Kaufman,
Evolutionary conservation of MHC class I and class II molecules--different yet the same.
1994,
Pubmed Kaufman,
Co-evolving genes in MHC haplotypes: the "rule" for nonmammalian vertebrates?
1999,
Pubmed Maruyama,
Genetic variability maintained by mutation and overdominant selection in finite populations.
1981,
Pubmed Muse,
Estimating synonymous and nonsynonymous substitution rates.
1996,
Pubmed Namikawa,
Isolation of Xenopus LMP-7 homologues. Striking allelic diversity and linkage to MHC.
1995,
Pubmed
,
Xenbase Neisig,
Allele-specific differences in the interaction of MHC class I molecules with transporters associated with antigen processing.
1996,
Pubmed Nonaka,
Evolution of proteasome subunits delta and LMP2: complementary DNA cloning and linkage analysis with MHC in lower vertebrates.
1997,
Pubmed
,
Xenbase Nonaka,
Major histocompatibility complex gene mapping in the amphibian Xenopus implies a primordial organization.
1997,
Pubmed
,
Xenbase Ohta,
Proteasome, transporter associated with antigen processing, and class I genes in the nurse shark Ginglymostoma cirratum: evidence for a stable class I region and MHC haplotype lineages.
2002,
Pubmed Ohta,
Two highly divergent ancient allelic lineages of the transporter associated with antigen processing (TAP) gene in Xenopus: further evidence for co-evolution among MHC class I region genes.
2003,
Pubmed
,
Xenbase Ohta,
Identification and genetic mapping of Xenopus TAP2 genes.
1999,
Pubmed
,
Xenbase Paquet,
Mutant MHC class I molecules define interactions between components of the peptide-loading complex.
2002,
Pubmed Parham,
Population biology of antigen presentation by MHC class I molecules.
1996,
Pubmed Parham,
Nature of polymorphism in HLA-A, -B, and -C molecules.
1988,
Pubmed Rozas,
DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis.
1999,
Pubmed Saper,
Refined structure of the human histocompatibility antigen HLA-A2 at 2.6 A resolution.
1991,
Pubmed Schwede,
SWISS-MODEL: An automated protein homology-modeling server.
2003,
Pubmed Sharp,
In search of molecular darwinism.
1997,
Pubmed Shum,
Modes of salmonid MHC class I and II evolution differ from the primate paradigm.
2001,
Pubmed Sobolev,
Automated analysis of interatomic contacts in proteins.
1999,
Pubmed Suzuki,
A method for detecting positive selection at single amino acid sites.
1999,
Pubmed Suzuki,
False-positive selection identified by ML-based methods: examples from the Sig1 gene of the diatom Thalassiosira weissflogii and the tax gene of a human T-cell lymphotropic virus.
2004,
Pubmed Thompson,
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.
1994,
Pubmed Turnquist,
HLA-B polymorphism affects interactions with multiple endoplasmic reticulum proteins.
2000,
Pubmed Williams,
Optimization of the MHC class I peptide cargo is dependent on tapasin.
2002,
Pubmed Wong,
Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites.
2004,
Pubmed Wu,
An analysis of the sequences of the variable regions of Bence Jones proteins and myeloma light chains and their implications for antibody complementarity.
1970,
Pubmed Yang,
Statistical methods for detecting molecular adaptation.
2000,
Pubmed Yang,
Codon-substitution models for heterogeneous selection pressure at amino acid sites.
2000,
Pubmed Yu,
An extensive region of an MHC class I alpha 2 domain loop influences interaction with the assembly complex.
1999,
Pubmed Zernich,
Natural HLA class I polymorphism controls the pathway of antigen presentation and susceptibility to viral evasion.
2004,
Pubmed Zhang,
Structural principles that govern the peptide-binding motifs of class I MHC molecules.
1998,
Pubmed
