Cargando…

Structural Re-Alignment in an Immunogenic Surface Region of Ricin A Chain

We compared structure alignments generated by several protein structure comparison programs to determine whether existing methods would satisfactorily align residues at a highly conserved position within an immunogenic loop in ribosome inactivating proteins (RIPs). Using default settings, structure...

Descripción completa

Detalles Bibliográficos
Autores principales: Zemla, Adam T., Ecale Zhou, Carol L.
Formato: Texto
Lenguaje:English
Publicado: Libertas Academica 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2735970/
https://www.ncbi.nlm.nih.gov/pubmed/19812763
_version_ 1782171289949044736
author Zemla, Adam T.
Ecale Zhou, Carol L.
author_facet Zemla, Adam T.
Ecale Zhou, Carol L.
author_sort Zemla, Adam T.
collection PubMed
description We compared structure alignments generated by several protein structure comparison programs to determine whether existing methods would satisfactorily align residues at a highly conserved position within an immunogenic loop in ribosome inactivating proteins (RIPs). Using default settings, structure alignments generated by several programs (CE, DaliLite, FATCAT, LGA, MAMMOTH, MATRAS, SHEBA, SSM) failed to align the respective conserved residues, although LGA reported correct residue-residue (R-R) correspondences when the beta-carbon (Cb) position was used as the point of reference in the alignment calculations. Further tests using variable points of reference indicated that points distal from the beta carbon along a vector connecting the alpha and beta carbons yielded rigid structural alignments in which residues known to be highly conserved in RIPs were reported as corresponding residues in structural comparisons between ricin A chain, abrin-A, and other RIPs. Results suggest that approaches to structure alignment employing alternate point representations corresponding to side chain position may yield structure alignments that are more consistent with observed conservation of functional surface residues than do standard alignment programs, which apply uniform criteria for alignment (i.e. alpha carbon (Ca) as point of reference) along the entirety of the peptide chain. We present the results of tests that suggest the utility of allowing user-specified points of reference in generating alternate structural alignments, and we present a web server for automatically generating such alignments: http://as2ts.llnl.gov/AS2TS/LGA/lga_pdblist_plots.html.
format Text
id pubmed-2735970
institution National Center for Biotechnology Information
language English
publishDate 2008
publisher Libertas Academica
record_format MEDLINE/PubMed
spelling pubmed-27359702009-09-14 Structural Re-Alignment in an Immunogenic Surface Region of Ricin A Chain Zemla, Adam T. Ecale Zhou, Carol L. Bioinform Biol Insights Methodology We compared structure alignments generated by several protein structure comparison programs to determine whether existing methods would satisfactorily align residues at a highly conserved position within an immunogenic loop in ribosome inactivating proteins (RIPs). Using default settings, structure alignments generated by several programs (CE, DaliLite, FATCAT, LGA, MAMMOTH, MATRAS, SHEBA, SSM) failed to align the respective conserved residues, although LGA reported correct residue-residue (R-R) correspondences when the beta-carbon (Cb) position was used as the point of reference in the alignment calculations. Further tests using variable points of reference indicated that points distal from the beta carbon along a vector connecting the alpha and beta carbons yielded rigid structural alignments in which residues known to be highly conserved in RIPs were reported as corresponding residues in structural comparisons between ricin A chain, abrin-A, and other RIPs. Results suggest that approaches to structure alignment employing alternate point representations corresponding to side chain position may yield structure alignments that are more consistent with observed conservation of functional surface residues than do standard alignment programs, which apply uniform criteria for alignment (i.e. alpha carbon (Ca) as point of reference) along the entirety of the peptide chain. We present the results of tests that suggest the utility of allowing user-specified points of reference in generating alternate structural alignments, and we present a web server for automatically generating such alignments: http://as2ts.llnl.gov/AS2TS/LGA/lga_pdblist_plots.html. Libertas Academica 2008-02-01 /pmc/articles/PMC2735970/ /pubmed/19812763 Text en Copyright © 2008 The authors. http://creativecommons.org/licenses/by/3.0 This article is an open-access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/3.0/).
spellingShingle Methodology
Zemla, Adam T.
Ecale Zhou, Carol L.
Structural Re-Alignment in an Immunogenic Surface Region of Ricin A Chain
title Structural Re-Alignment in an Immunogenic Surface Region of Ricin A Chain
title_full Structural Re-Alignment in an Immunogenic Surface Region of Ricin A Chain
title_fullStr Structural Re-Alignment in an Immunogenic Surface Region of Ricin A Chain
title_full_unstemmed Structural Re-Alignment in an Immunogenic Surface Region of Ricin A Chain
title_short Structural Re-Alignment in an Immunogenic Surface Region of Ricin A Chain
title_sort structural re-alignment in an immunogenic surface region of ricin a chain
topic Methodology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2735970/
https://www.ncbi.nlm.nih.gov/pubmed/19812763
work_keys_str_mv AT zemlaadamt structuralrealignmentinanimmunogenicsurfaceregionofricinachain
AT ecalezhoucaroll structuralrealignmentinanimmunogenicsurfaceregionofricinachain