Dataset Information

BlockLogo: visualization of peptide and sequence motif conservation.

ABSTRACT: BlockLogo is a web-server application for the visualization of protein and nucleotide fragments, continuous protein sequence motifs, and discontinuous sequence motifs using calculation of block entropy from multiple sequence alignments. The user input consists of a multiple sequence alignment, selection of motif positions, type of sequence, and output format definition. The output has BlockLogo along with the sequence logo, and a table of motif frequencies. We deployed BlockLogo as an online application and have demonstrated its utility through examples that show visualization of T-cell epitopes and B-cell epitopes (both continuous and discontinuous). Our additional example shows a visualization and analysis of structural motifs that determine the specificity of peptide binding to HLA-DR molecules. The BlockLogo server also employs selected experimentally validated prediction algorithms to enable on-the-fly prediction of MHC binding affinity to 15 common HLA class I and class II alleles as well as visual analysis of discontinuous epitopes from multiple sequence alignments. It enables the visualization and analysis of structural and functional motifs that are usually described as regular expressions. It provides a compact view of discontinuous motifs composed of distant positions within biological sequences. BlockLogo is available at: http://research4.dfci.harvard.edu/cvc/blocklogo/ and http://met-hilab.bu.edu/blocklogo/.

SUBMITTER: Olsen LR

PROVIDER: S-EPMC3856553 | biostudies-literature | 2013 Dec

REPOSITORIES: biostudies-literature

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BlockLogo: visualization of peptide and sequence motif conservation.

Olsen Lars Rønn LR Kudahl Ulrich Johan UJ Simon Christian C Sun Jing J Schönbach Christian C Reinherz Ellis L EL Zhang Guang Lan GL Brusic Vladimir V

Journal of immunological methods 20130831

BlockLogo is a web-server application for the visualization of protein and nucleotide fragments, continuous protein sequence motifs, and discontinuous sequence motifs using calculation of block entropy from multiple sequence alignments. The user input consists of a multiple sequence alignment, selection of motif positions, type of sequence, and output format definition. The output has BlockLogo along with the sequence logo, and a table of motif frequencies. We deployed BlockLogo as an online app ...[more]

PMID: 24001880

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Project description:Antiphospholipid antibody syndrome is an autoimmune disease characterized by the presence of so-called antiphospholipid antibodies and clinical manifestations such as recurrent thromboembolic or pregnancy complications. Although the main antigenic determinant for antiphospholipid antibodies has been identified as the β-2-glycoprotein 1 (β2GP1), the precise epitope recognized by antiphospholipid antibodies still remains largely unknown. In the study herein, we wanted to identify a sequence in domain I of β2GP1 able to induce the proliferation of CD4+ T cells isolated from antiphospholipid antibody syndrome patients, but not from healthy donors, and to interact with antiphospholipid antibodies. We have characterized a sequence in domain I of β2GP1 that triggers CD4+ T-cell proliferation. A comparison of this sequence with the previously reported binding of antiphospholipid antibodies to discontinuous epitope R39-R43 reveals the presence of an indeterminate motif in β2GP1, in which the polarity determines the characteristics and specificity of antiphospholipid antibodies-interacting motifs. Using point mutations, we characterized the main antiphospholipid antibodies-interacting motif as ϕϕϕζζFxC, but also established ϕϕϕζζFxϕ-related motifs as potential antiphospholipid antibodies epitopes, in which ϕ represents nonpolar residues and ζ polar residues, with charges of the residues not being involved. Of specific importance, these different motifs are present at least once in all antiphospholipid antibodies-related receptors described so far. We have further demonstrated, in vitro, that peptides and domains of β2GP1 containing these motifs were able to interact with antiphospholipid antibodies and inhibit their monocyte activating activity. These results established that the antiphospholipid antibodies-interacting motifs are determined by the polarity, but not by the sequence or charge, of amino acids. These data could also contribute to the future development of more sensitive and specific diagnostic tools for antiphospholipid antibody syndrome determination and potential peptide- or β2GP1 domain-based clinical therapies.

Dataset Information

BlockLogo: visualization of peptide and sequence motif conservation.

Publications

BlockLogo: visualization of peptide and sequence motif conservation.

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