RESUMO
The structural determination of peptide:HLA (human leucocyte antigen) class I complexes by X-ray crystallography has provided valuable information for understanding how peptides bind to individual HLA class I molecules and how this may influence the immune response. We compared 101 crystal structures of 9-mer peptide:HLA class I complexes available in the protein data bank (PDB) by performing a contact analysis using the Contact Map Analysis webserver http://ligin.weizmann.ac.il/cma. An InterSystems Caché 'post-relational' database containing residue position, amino acid (AA) and buried surface that contact a particular peptide position was then created allowing data comparison for all the structures (Pocketcheck). The analysis illustrates that the HLA class I residues 24, 45, 63 and 67 show high contact frequencies to both the p1 and/or p2 position of bound peptides, indicating that they might influence the nature of a peptide anchor. To determine the influence of these residues we utilized soluble HLA technology and mass spectrometry to analyze peptides derived from HLA-B*44:06 since it differs from the previously described allele B*44:02 by seven AA exchanges located in the alpha 1 domain (residues 24, 32, 41, 45, 63, 67 and 80). HLA-B*44:06 features an anchor motif of P or A at p2 and Y or W at the C-terminal. Additionally B*44:06-derived peptides feature an auxiliary anchor motif at p1, comprising D or E. Our results illustrate that structural analysis can provide valuable information to understand allogenicity and provides a further step towards intelligent HLA mismatching.
Assuntos
Antígenos de Histocompatibilidade Classe I/química , Antígenos de Histocompatibilidade Classe I/imunologia , Peptídeos/química , Peptídeos/imunologia , Alelos , Sequência de Aminoácidos , Aminoácidos/metabolismo , Linhagem Celular , Biologia Computacional , Bases de Dados de Proteínas , Antígenos de Histocompatibilidade Classe I/genética , Humanos , Ligantes , Dados de Sequência Molecular , Polimorfismo Genético , Ligação ProteicaRESUMO
The new allele HLA-B*35:87 was generated by recombination between HLA-B*35:01 and B*08:01 in intron 2.
Assuntos
Alelos , Antígenos HLA-B/classificação , Antígenos HLA-B/genética , Íntrons/genética , Recombinação Genética , Humanos , Dados de Sequência Molecular , Alinhamento de Sequência , Homologia de Sequência do Ácido NucleicoRESUMO
In this study we sequenced the bound peptides from three alleles belonging to the HLA-A*74 group (HLA-A*74:04, A*74:06 and A*74:07) that are distinguished by four polymorphic residues within the peptide-binding region. Our data illustrates that A*74:04 exhibits preference for L, M or I at P2 and L, S or P at PΩ, while for A*74:07 the P2 anchor prefers L, P or I and the PΩ anchor S, P, L. In contrast A*74:06 features a P2 anchor motif of S or L, while a PΩ anchor could not be defined; however, a preference for polar residues S, T, Q or the charged residue R at the PΩ position could be detected.
Assuntos
Antígenos HLA-A/genética , Peptídeos/genética , Alelos , Motivos de Aminoácidos , Sequência de Aminoácidos , Sítios de Ligação , Antígenos HLA-A/química , Antígenos HLA-A/imunologia , Humanos , Dados de Sequência Molecular , Peptídeos/química , Peptídeos/imunologiaRESUMO
The BRCA1 C-terminal region contains a duplicated globular domain termed BRCT that is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions with DNA strand breaks. The sequence and functional diversity of the BRCT superfamily suggests that BRCT domains are evolutionarily convenient interaction modules.
Assuntos
Proteína BRCA1/química , Proteínas Supressoras de Tumor , Ubiquitina-Proteína Ligases , Sequência de Aminoácidos , Proteína BRCA1/fisiologia , Proteínas de Bactérias/química , Biopolímeros , Neoplasias da Mama/genética , Proteínas de Transporte/química , Proteínas de Transporte/fisiologia , Proteínas de Ciclo Celular/química , Dano ao DNA , DNA Ligases/química , DNA Nucleotidilexotransferase/química , DNA Nucleotidilexotransferase/fisiologia , Reparo do DNA , Proteínas de Ligação a DNA/química , Evolução Molecular , Feminino , Proteínas Fúngicas/química , Genes BRCA1 , Humanos , Modelos Moleculares , Dados de Sequência Molecular , Mutação de Sentido Incorreto , Síndromes Neoplásicas Hereditárias/genética , Proteínas Nucleares , Poli(ADP-Ribose) Polimerases/química , Conformação Proteica , Estrutura Terciária de Proteína , Alinhamento de Sequência , Homologia de Sequência de Aminoácidos , Relação Estrutura-Atividade , Proteína 1 Complementadora Cruzada de Reparo de Raio-XRESUMO
d-alanine-d-lactate ligase from Enterococcus faecium BM4147 is directly responsible for the biosynthesis of alternate cell-wall precursors in bacteria, which are resistant to the glycopeptide antibiotic vancomycin. The crystal structure has been determined with data extending to 2.5-A resolution. This structure shows that the active site has unexpected interactions and is distinct from previous models for d-alanyl-d-lactate ligase mechanistic studies. It appears that the preference of the enzyme for lactate as a ligand over d-alanine could be mediated by electrostatic effects and/or a hydrogen-bonding network, which principally involve His-244. The structure of d-alanyl-d-lactate ligase provides a revised interpretation of the molecular events that lead to vancomycin resistance.
Assuntos
Proteínas de Bactérias/química , Carbono-Oxigênio Ligases/química , Enterococcus faecium/efeitos dos fármacos , Resistência a Vancomicina , Cristalografia por Raios X , Ligação de Hidrogênio , Conformação ProteicaRESUMO
A recombinant form of Enterococcus facieum BM4147 D-alanine-D-lactate ligase (VanA) has been prepared and crystallized. VanA was found to crystallize only in the presence of a phosphinate inhibitor analogue of D-alanine-D-alanine. The crystals grow in 40-45% ammonium sulfate, 0.1 M 3-(N-morpholino)-propanesulfonic acid pH 6.0 and reach dimensions of 0.4 x 0.2 x 0.1 mm. The crystals diffract to at least 2.5 A and are in the centred orthorhombic space group C222(1), with unit-cell dimensions a = 123.2, b = 225.4, c = 72.4 A.
