Recognition of higher order patterns in proteins: immunologic kernels
By applying analysis of the principal components of amino acid physical properties we predicted cathepsin cleavage sites, MHC binding affinity, and probability of B-cell epitope binding of peptides in tetanus toxin and in ten diverse additional proteins. Cross-correlation of these metrics, for pepti...
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| Veröffentlicht in: | PloS one 2013-07, Vol.8 (7), p.e70115 |
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| description | By applying analysis of the principal components of amino acid physical properties we predicted cathepsin cleavage sites, MHC binding affinity, and probability of B-cell epitope binding of peptides in tetanus toxin and in ten diverse additional proteins. Cross-correlation of these metrics, for peptides of all possible amino acid index positions, each evaluated in the context of a ±25 amino acid flanking region, indicated that there is a strongly repetitive pattern of short peptides of approximately thirty amino acids each bounded by cathepsin cleavage sites and each comprising B-cell linear epitopes, MHC-I and MHC-II binding peptides. Such "immunologic kernel" peptides comprise all signals necessary for adaptive immunologic cognition, response and recall. The patterns described indicate a higher order spatial integration that forms a symbolic logic coordinating the adaptive immune system. |
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Cross-correlation of these metrics, for peptides of all possible amino acid index positions, each evaluated in the context of a ±25 amino acid flanking region, indicated that there is a strongly repetitive pattern of short peptides of approximately thirty amino acids each bounded by cathepsin cleavage sites and each comprising B-cell linear epitopes, MHC-I and MHC-II binding peptides. Such "immunologic kernel" peptides comprise all signals necessary for adaptive immunologic cognition, response and recall. The patterns described indicate a higher order spatial integration that forms a symbolic logic coordinating the adaptive immune system.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0070115</identifier><identifier>PMID: 23922927</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Adaptive systems ; Amino acids ; Antigens ; B-Lymphocytes - immunology ; B-Lymphocytes - metabolism ; Binding ; Biology ; Cathepsins - chemistry ; Cathepsins - metabolism ; Cleavage ; Cluster Analysis ; Cognition ; Dendritic cells ; Epitopes ; Epitopes - chemistry ; Epitopes - immunology ; Epitopes - metabolism ; Epitopes, B-Lymphocyte ; Histocompatibility Antigens Class I - immunology ; Histocompatibility Antigens Class I - metabolism ; Histocompatibility Antigens Class II - immunology ; Histocompatibility Antigens Class II - metabolism ; Humans ; Immune system ; Kernels ; Lymphocytes B ; Major histocompatibility complex ; Models, Immunological ; Pattern recognition ; Peptides ; Peptides - chemistry ; Peptides - immunology ; Peptides - metabolism ; Physical properties ; Probability ; Protein Binding - immunology ; Proteins ; Proteins - chemistry ; Proteins - immunology ; Proteins - metabolism ; Proteolysis ; Recall ; Tetanus ; Tetanus toxin ; Tetanus Toxin - chemistry ; Tetanus Toxin - immunology ; Tetanus Toxin - metabolism ; Time series</subject><ispartof>PloS one, 2013-07, Vol.8 (7), p.e70115</ispartof><rights>2013 Bremel, Homan. This is an open-access article distributed under the terms of the Creative Commons Attribution License: https://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2013 Bremel, Homan 2013 Bremel, Homan</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c526t-44037cce3650676f849e9762cda147dafa6201a699a2412532ae3818bfe1401b3</citedby><cites>FETCH-LOGICAL-c526t-44037cce3650676f849e9762cda147dafa6201a699a2412532ae3818bfe1401b3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3726486/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3726486/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2096,2915,23845,27901,27902,53766,53768,79342,79343</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/23922927$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Bremel, Robert D</creatorcontrib><creatorcontrib>Homan, E Jane</creatorcontrib><title>Recognition of higher order patterns in proteins: immunologic kernels</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>By applying analysis of the principal components of amino acid physical properties we predicted cathepsin cleavage sites, MHC binding affinity, and probability of B-cell epitope binding of peptides in tetanus toxin and in ten diverse additional proteins. Cross-correlation of these metrics, for peptides of all possible amino acid index positions, each evaluated in the context of a ±25 amino acid flanking region, indicated that there is a strongly repetitive pattern of short peptides of approximately thirty amino acids each bounded by cathepsin cleavage sites and each comprising B-cell linear epitopes, MHC-I and MHC-II binding peptides. Such "immunologic kernel" peptides comprise all signals necessary for adaptive immunologic cognition, response and recall. The patterns described indicate a higher order spatial integration that forms a symbolic logic coordinating the adaptive immune system.</description><subject>Adaptive systems</subject><subject>Amino acids</subject><subject>Antigens</subject><subject>B-Lymphocytes - immunology</subject><subject>B-Lymphocytes - metabolism</subject><subject>Binding</subject><subject>Biology</subject><subject>Cathepsins - chemistry</subject><subject>Cathepsins - metabolism</subject><subject>Cleavage</subject><subject>Cluster Analysis</subject><subject>Cognition</subject><subject>Dendritic cells</subject><subject>Epitopes</subject><subject>Epitopes - chemistry</subject><subject>Epitopes - immunology</subject><subject>Epitopes - metabolism</subject><subject>Epitopes, B-Lymphocyte</subject><subject>Histocompatibility Antigens Class I - immunology</subject><subject>Histocompatibility Antigens Class I - metabolism</subject><subject>Histocompatibility Antigens Class II - immunology</subject><subject>Histocompatibility Antigens Class II - metabolism</subject><subject>Humans</subject><subject>Immune system</subject><subject>Kernels</subject><subject>Lymphocytes B</subject><subject>Major histocompatibility complex</subject><subject>Models, Immunological</subject><subject>Pattern recognition</subject><subject>Peptides</subject><subject>Peptides - chemistry</subject><subject>Peptides - immunology</subject><subject>Peptides - metabolism</subject><subject>Physical properties</subject><subject>Probability</subject><subject>Protein Binding - immunology</subject><subject>Proteins</subject><subject>Proteins - chemistry</subject><subject>Proteins - immunology</subject><subject>Proteins - metabolism</subject><subject>Proteolysis</subject><subject>Recall</subject><subject>Tetanus</subject><subject>Tetanus toxin</subject><subject>Tetanus Toxin - chemistry</subject><subject>Tetanus Toxin - immunology</subject><subject>Tetanus Toxin - metabolism</subject><subject>Time series</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2013</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><sourceid>DOA</sourceid><recordid>eNp1UVtrHCEUltLSXNp_ENqBPu_Wo46OfSiEkKSBQKEkz-I6Z2bdzOpUZwv993Wzk5A89EXlnO-GHyFnQJfAFXzdxF0KdliOMeCSUkUB6jfkGDRnC8kof_vifUROct5QWvNGyvfkiHHNmGbqmFz-Qhf74CcfQxW7au37NaYqpraco50mTCFXPlRjihP6kL9VfrvdhTjE3rvqoaxxyB_Iu84OGT_O9ym5v7q8u_ixuP15fXNxfrtwNZPTQgjKlXPIZU2lkl0jNGolmWstCNXazpawYKXWlglgNWcWeQPNqkMQFFb8lHw-6I5DzGb-gWygCGsthaoL4uaAaKPdmDH5rU1_TbTePA5i6o1Nk3cDmmLQWFxBA1oIAY0FXVw5lbXgVMi91vfZbbfaYuswTMkOr0Rfb4Jfmz7-MVwxKRpZBL7MAin-3mGe_hNZHFAuxZwTds8OQM2-6ieW2Vdt5qoL7dPLdM-kp275P3z3pcs</recordid><startdate>20130729</startdate><enddate>20130729</enddate><creator>Bremel, Robert D</creator><creator>Homan, E Jane</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20130729</creationdate><title>Recognition of higher order patterns in proteins: immunologic kernels</title><author>Bremel, Robert D ; Homan, E Jane</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c526t-44037cce3650676f849e9762cda147dafa6201a699a2412532ae3818bfe1401b3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2013</creationdate><topic>Adaptive systems</topic><topic>Amino acids</topic><topic>Antigens</topic><topic>B-Lymphocytes - 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| subjects | Adaptive systems Amino acids Antigens B-Lymphocytes - immunology B-Lymphocytes - metabolism Binding Biology Cathepsins - chemistry Cathepsins - metabolism Cleavage Cluster Analysis Cognition Dendritic cells Epitopes Epitopes - chemistry Epitopes - immunology Epitopes - metabolism Epitopes, B-Lymphocyte Histocompatibility Antigens Class I - immunology Histocompatibility Antigens Class I - metabolism Histocompatibility Antigens Class II - immunology Histocompatibility Antigens Class II - metabolism Humans Immune system Kernels Lymphocytes B Major histocompatibility complex Models, Immunological Pattern recognition Peptides Peptides - chemistry Peptides - immunology Peptides - metabolism Physical properties Probability Protein Binding - immunology Proteins Proteins - chemistry Proteins - immunology Proteins - metabolism Proteolysis Recall Tetanus Tetanus toxin Tetanus Toxin - chemistry Tetanus Toxin - immunology Tetanus Toxin - metabolism Time series |
| title | Recognition of higher order patterns in proteins: immunologic kernels |
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