Secondary structure and 3D homology modeling of swine leukocyte antigen class 2 (SLA-2) molecules

Feng-shan, Gao; Chongbo, Xu; Long, Yi-hou; Xia, Chun

doi:10.1016/j.imbio.2008.11.001

Cited by 10 publications

(6 citation statements)

References 14 publications

(15 reference statements)

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“…The SLA-1*0401 gene (EU170457) was cloned from PK-15 cells. The PCR primers and conditions were described previously (15). The PCR product was sequenced, ligated into the pET21a vector (Novagen), and transformed into Escherichia coli strain BL21(DE3).…”

Section: Synthesis Of Viral Peptidesmentioning

confidence: 99%

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Crystal Structure of Swine Major Histocompatibility Complex Class I SLA-1*0401 and Identification of 2009 Pandemic Swine-Origin Influenza A H1N1 Virus Cytotoxic T Lymphocyte Epitope Peptides

Zhang

Feng

et al. 2011

J Virol

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The presentation of viral epitopes to cytotoxic T lymphocytes (CTLs) by swine leukocyte antigen class I (SLA I) is crucial for swine immunity. To illustrate the structural basis of swine CTL epitope presentation, the first SLA crystal structures, SLA-1*0401, complexed with peptides derived from either 2009 pandemic H1N1 (pH1N1) swine-origin influenza A virus (S-OIV NW9 ; NSDTVGWSW) or Ebola virus (Ebola AY9 ; ATAAATEAY) were determined in this study. The overall peptide-SLA-1*0401 structures resemble, as expected, the general conformations of other structure-solved peptide major histocompatibility complexes (pMHC). The major distinction of SLA-1*0401 is that Arg 156 has a "one-ballot veto" function in peptide binding, due to its flexible side chain. S-OIV NW9 and Ebola AY9 bind SLA-1*0401 with similar conformations but employ different water molecules to stabilize their binding. The side chain of P7 residues in both peptides is exposed, indicating that the epitopes are "featured" peptides presented by this SLA. Further analyses showed that SLA-1*0401 and human leukocyte antigen (HLA) class I HLA-A*0101 can present the same peptides, but in different conformations, demonstrating cross-species epitope presentation. CTL epitope peptides derived from 2009 pandemic S-OIV were screened and evaluated by the in vitro refolding method. Three peptides were identified as potential cross-species influenza virus (IV) CTL epitopes. The binding motif of SLA-1*0401 was proposed, and thermostabilities of key peptide-SLA-1*0401 complexes were analyzed by circular dichroism spectra. Our results not only provide the structural basis of peptide presentation by SLA I but also identify some IV CTL epitope peptides. These results will benefit both vaccine development and swine organ-based xenotransplantation.

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Section: Synthesis Of Viral Peptidesmentioning

confidence: 99%

“…The gene fragment encoding the mature peptide of swine ␤ 2 -microglobulin (s␤ 2 m) was amplified from plasmid p2X-␤2m, which we constructed previously (15). The PCR product was sequenced, ligated into the pET21a vector, and transformed into E. coli strain BL21(DE3).…”

Section: Synthesis Of Viral Peptidesmentioning

confidence: 99%

Crystal Structure of Swine Major Histocompatibility Complex Class I SLA-1*0401 and Identification of 2009 Pandemic Swine-Origin Influenza A H1N1 Virus Cytotoxic T Lymphocyte Epitope Peptides

Zhang

Feng

et al. 2011

J Virol

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“…The crystal structure of the SLA class I molecules has not been reported and detailed data on the secondary and tertiary structure are still at the prediction stage (17). In this study, with reference to human HLA‐A2 crystal structure data, the possible functional sites of the SLA‐2‐HB alleles were predicted by comparison with human HLA‐A2 and HLA‐B15 and rat H‐2K1 (Fig.…”

Section: Gene Groups Of Sla‐2 Allelesmentioning

confidence: 99%

Analyzing the genetic characteristics and function of the swine leukocyte antigen 2 gene in a Chinese inbreed of pigs

Feng-shan

Bai

Gong

et al. 2012

Microbiology and Immunology

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To study the genetic characteristics and function of swine leukocyte antigen (SLA) class I from the Hebao pig, a rare inbreed in China, a pair of primers was designed to amplify the SLA-2 gene (SLA-2-HB) and then the genetic characteristics of the gene were analyzed. The 3D homology modeling was used to analyze the structure and function of SLA-2-HB proteins. After cloning, sequencing and computer analysis, four SLA-2-HB alleles were found, all of 1119 bp. Sites 3-1097 were an open reading frame encoding 364 amino acids with two sets of intra-chain disulfide bonds comprising four cysteines situated in sites 125, 188, 227 and 283. By alignment of SLA-2-HB sequences with other SLA-2 alleles in the IPD database, 11 key variable amino acid sites were found in the extracellular domain of the SLA-2-HB alleles at sites 23(F), 24(I), 43(A), 44(K), 50(Q), 73(N), 95(I), 114(R), 155(G), 156(E) and 216(S), which could be used to differentiate other SLA-2 alleles. The 3D homology modeling demonstrated that the eight of 11 key variable amino acid sites were all in antigenic binding groove of SLA-2-HB proteins. The amino acid identities between SLA-2-HB and other SLA-2, SLA-1 and SLA-3 alleles were 86.2-97.0%, 85.0-93.9% and 83.3-88.6%, respectively. The phylogenetic tree of SLA-2-HB showed that it was relatively independent of the other SLA-2 genes. Furthermore, the SLA-2-HB alleles were similar to HLA-B15 and HLA-A2 functional domains and preserved some functional sites of HLA-A2. It was concluded that SLA-2-HB are novel alleles of SLA-2 and that the Hebao pig might have evolved independently in China.

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“…The phylogenetic tree showed that the SLA 2 HB alleles were situated on an independent branch, which indicated that the Hebao pig might have evolved independently in its enclosed mountain terrain. The crystal structure of the SLA class I molecules has not been reported and detailed data on the second ary and tertiary structure are still at the prediction stage [15]. In this study, with reference to human HLA A2 crystal structure data, the possible functional sites of the SLA 2 HB alleles were predicted by com parison with human HLA A2 and HLA B15 and rat H 2K1 (Fig.…”

Section: Discussionmentioning

confidence: 88%

Molecular characteristics of the SLA-2 gene from Chinese Hebao pigs

et al. 2012

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To study the molecular characteristics of swine leukocyte antigen (SLA) class I from the Hebao pig, a rare inbreed in China, a pair of primers was designed to amplify the SLA 2 gene (SLA 2 HB) and then the molecular characteristics of the gene were analyzed by computer. After cloning, sequencing and computer analysis, four SLA 2 HB alleles were found, all of 1119 bp. Sites 3-1097 were an open reading frame encod ing 364 amino acids with two sets of intra chain disulfide bonds comprising four cysteines situated in sites 125, 188, 227 and 283. By alignment of SLA 2 HB sequences with other SLA 2 alleles in the DNA Data Bank of Japan/European Molecular Biology Laboratory/GenBank database, nine key variable amino acid sites were found in the extracellular domain of the SLA 2 HB alleles at sites 23(F), 24(I), 43(A), 44(K), 50(Q), 73(N), 95(I), 114(R) and 216(S), which could be used to differentiate other SLA 2 alleles. The amino acid identities between SLA 2 HB and other SLA 2, SLA 3 and SLA 1 alleles were 87.1-97.0%, 85.0-93.9% and 83.3-88.6%, respectively. The phylogenetic tree of SLA 2 HB showed that it was relatively independent of the other SLA 2 genes. Furthermore, the SLA 2 HB alleles were similar to HLA B15 and HLA A2 functional domains and preserved some functional sites of HLA A2. It was concluded that SLA 2 HB is an allele of SLA 2 and that the Hebao pig might have evolved independently in China.

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Secondary structure and 3D homology modeling of swine leukocyte antigen class 2 (SLA-2) molecules

Cited by 10 publications

References 14 publications

Crystal Structure of Swine Major Histocompatibility Complex Class I SLA-1*0401 and Identification of 2009 Pandemic Swine-Origin Influenza A H1N1 Virus Cytotoxic T Lymphocyte Epitope Peptides

Crystal Structure of Swine Major Histocompatibility Complex Class I SLA-1*0401 and Identification of 2009 Pandemic Swine-Origin Influenza A H1N1 Virus Cytotoxic T Lymphocyte Epitope Peptides

Analyzing the genetic characteristics and function of the swine leukocyte antigen 2 gene in a Chinese inbreed of pigs

Molecular characteristics of the SLA-2 gene from Chinese Hebao pigs

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