The Channel in Transporters is Formed by Residues That Are Rare in Transmembrane Helices
Transmembrane transport is an essential component of the cell life. Many genes encoding known or putative transport proteins are found in bacterial genomes. In most cases their substrate specificity is not experimentally determined and only approximately predicted by comparative genomic analysis. Ev...
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| Veröffentlicht in: | In silico biology 2003, Vol.3 (1-2), p.197-204 |
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| container_title | In silico biology |
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| creator | Kalinina, Olga V. Makeev, Vsevolod J. Sutormin, Roman A. Gelfand, Mikhail S. Rakhmaninova, Aleksandra B. |
| description | Transmembrane transport is an essential component of the cell life.
Many genes encoding known or putative transport proteins are found in bacterial
genomes. In most cases their substrate specificity is not experimentally
determined and only approximately predicted by comparative genomic analysis.
Even less is known about the 3D structure of transporters. Nevertheless, the
published experimental data demonstrate that channel-forming residues
determine the substrate specificity of secondary transporters and analysis of
these residues would provide better understanding of the transport mechanism.
We developed a simple computational method for identification of
channel-forming residues in transporter sequences. It is based on the analysis
of amino acids frequencies in bacterial secondary transporters. We applied this
method to a variety of transmembrane proteins with resolved 3D structure. The
predictions are in sufficiently good agreement with the real protein
structure. |
| doi_str_mv | 10.3233/ISB-00088 |
| format | Article |
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Many genes encoding known or putative transport proteins are found in bacterial
genomes. In most cases their substrate specificity is not experimentally
determined and only approximately predicted by comparative genomic analysis.
Even less is known about the 3D structure of transporters. Nevertheless, the
published experimental data demonstrate that channel-forming residues
determine the substrate specificity of secondary transporters and analysis of
these residues would provide better understanding of the transport mechanism.
We developed a simple computational method for identification of
channel-forming residues in transporter sequences. It is based on the analysis
of amino acids frequencies in bacterial secondary transporters. We applied this
method to a variety of transmembrane proteins with resolved 3D structure. The
predictions are in sufficiently good agreement with the real protein
structure.</description><identifier>ISSN: 1386-6338</identifier><identifier>EISSN: 1434-3207</identifier><identifier>DOI: 10.3233/ISB-00088</identifier><identifier>PMID: 14524337</identifier><language>eng</language><publisher>London, England: SAGE Publications</publisher><subject>Algorithms ; Amino Acid Sequence ; ATP-Binding Cassette Transporters - chemistry ; Bacterial Proteins - chemistry ; Bacterial Proteins - physiology ; Biological Transport ; Ion Channels - chemistry ; Ion Channels - physiology ; Membrane Proteins - chemistry ; Membrane Proteins - physiology ; Models, Molecular ; Models, Theoretical ; Peptide Fragments - chemistry ; Protein Conformation ; Protein Structure, Secondary</subject><ispartof>In silico biology, 2003, Vol.3 (1-2), p.197-204</ispartof><rights>IOS Press. All rights reserved</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>315,781,785,4025,27925,27926,27927</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/14524337$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Kalinina, Olga V.</creatorcontrib><creatorcontrib>Makeev, Vsevolod J.</creatorcontrib><creatorcontrib>Sutormin, Roman A.</creatorcontrib><creatorcontrib>Gelfand, Mikhail S.</creatorcontrib><creatorcontrib>Rakhmaninova, Aleksandra B.</creatorcontrib><title>The Channel in Transporters is Formed by Residues That Are Rare in Transmembrane Helices</title><title>In silico biology</title><addtitle>In Silico Biol</addtitle><description>Transmembrane transport is an essential component of the cell life.
Many genes encoding known or putative transport proteins are found in bacterial
genomes. In most cases their substrate specificity is not experimentally
determined and only approximately predicted by comparative genomic analysis.
Even less is known about the 3D structure of transporters. Nevertheless, the
published experimental data demonstrate that channel-forming residues
determine the substrate specificity of secondary transporters and analysis of
these residues would provide better understanding of the transport mechanism.
We developed a simple computational method for identification of
channel-forming residues in transporter sequences. It is based on the analysis
of amino acids frequencies in bacterial secondary transporters. We applied this
method to a variety of transmembrane proteins with resolved 3D structure. The
predictions are in sufficiently good agreement with the real protein
structure.</description><subject>Algorithms</subject><subject>Amino Acid Sequence</subject><subject>ATP-Binding Cassette Transporters - chemistry</subject><subject>Bacterial Proteins - chemistry</subject><subject>Bacterial Proteins - physiology</subject><subject>Biological Transport</subject><subject>Ion Channels - chemistry</subject><subject>Ion Channels - physiology</subject><subject>Membrane Proteins - chemistry</subject><subject>Membrane Proteins - physiology</subject><subject>Models, Molecular</subject><subject>Models, Theoretical</subject><subject>Peptide Fragments - chemistry</subject><subject>Protein Conformation</subject><subject>Protein Structure, Secondary</subject><issn>1386-6338</issn><issn>1434-3207</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2003</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFUT1PwzAUtBCIlsLAH0Ce2AK2n524Y6korVQJqQSJzbITh6bKF3Yy9N_jQitGlndvuHe6e4fQLSUPwAAeV29PESFEyjM0phx4BIwk52EHGUcxgByhK-93Bwpn_BKNKBeMAyRj9JFuLZ5vddPYCpcNTp1ufNe63jqPS48Xrattjs0eb6wv88F6nG51j2fO4o0O43RT29oEtHhpqzKz_hpdFLry9uaIE_S-eE7ny2j9-rKaz9ZRRyXvIw2agMxkbIwBrmMQlFGTGJ6zXOuCyKKIeWynQrMk44QKKkQWJ5JxbSARAibo_le3c-1XsNeruvSZrargpR28SkTCYsGm_xLpVAhOBQTi3ZE4mJBdda6stdur09P-lLz-tGrXDq4JCRUl6tCGCm2onzbgG4Cqd68</recordid><startdate>2003</startdate><enddate>2003</enddate><creator>Kalinina, Olga V.</creator><creator>Makeev, Vsevolod J.</creator><creator>Sutormin, Roman A.</creator><creator>Gelfand, Mikhail S.</creator><creator>Rakhmaninova, Aleksandra B.</creator><general>SAGE Publications</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>7QL</scope><scope>7QO</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>P64</scope><scope>7X8</scope></search><sort><creationdate>2003</creationdate><title>The Channel in Transporters is Formed by Residues That Are Rare in Transmembrane Helices</title><author>Kalinina, Olga V. ; Makeev, Vsevolod J. ; Sutormin, Roman A. ; Gelfand, Mikhail S. ; Rakhmaninova, Aleksandra B.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-p184t-a3a038c86bbb34a635121b7b4d2daaf08ff646e95a27c4015155c67824ab37553</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2003</creationdate><topic>Algorithms</topic><topic>Amino Acid Sequence</topic><topic>ATP-Binding Cassette Transporters - chemistry</topic><topic>Bacterial Proteins - chemistry</topic><topic>Bacterial Proteins - physiology</topic><topic>Biological Transport</topic><topic>Ion Channels - chemistry</topic><topic>Ion Channels - physiology</topic><topic>Membrane Proteins - chemistry</topic><topic>Membrane Proteins - physiology</topic><topic>Models, Molecular</topic><topic>Models, Theoretical</topic><topic>Peptide Fragments - chemistry</topic><topic>Protein Conformation</topic><topic>Protein Structure, Secondary</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Kalinina, Olga V.</creatorcontrib><creatorcontrib>Makeev, Vsevolod J.</creatorcontrib><creatorcontrib>Sutormin, Roman A.</creatorcontrib><creatorcontrib>Gelfand, Mikhail S.</creatorcontrib><creatorcontrib>Rakhmaninova, Aleksandra B.</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>In silico biology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Kalinina, Olga V.</au><au>Makeev, Vsevolod J.</au><au>Sutormin, Roman A.</au><au>Gelfand, Mikhail S.</au><au>Rakhmaninova, Aleksandra B.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>The Channel in Transporters is Formed by Residues That Are Rare in Transmembrane Helices</atitle><jtitle>In silico biology</jtitle><addtitle>In Silico Biol</addtitle><date>2003</date><risdate>2003</risdate><volume>3</volume><issue>1-2</issue><spage>197</spage><epage>204</epage><pages>197-204</pages><issn>1386-6338</issn><eissn>1434-3207</eissn><abstract>Transmembrane transport is an essential component of the cell life.
Many genes encoding known or putative transport proteins are found in bacterial
genomes. In most cases their substrate specificity is not experimentally
determined and only approximately predicted by comparative genomic analysis.
Even less is known about the 3D structure of transporters. Nevertheless, the
published experimental data demonstrate that channel-forming residues
determine the substrate specificity of secondary transporters and analysis of
these residues would provide better understanding of the transport mechanism.
We developed a simple computational method for identification of
channel-forming residues in transporter sequences. It is based on the analysis
of amino acids frequencies in bacterial secondary transporters. We applied this
method to a variety of transmembrane proteins with resolved 3D structure. The
predictions are in sufficiently good agreement with the real protein
structure.</abstract><cop>London, England</cop><pub>SAGE Publications</pub><pmid>14524337</pmid><doi>10.3233/ISB-00088</doi><tpages>8</tpages></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1386-6338 |
| ispartof | In silico biology, 2003, Vol.3 (1-2), p.197-204 |
| issn | 1386-6338 1434-3207 |
| language | eng |
| recordid | cdi_proquest_miscellaneous_75726529 |
| source | MEDLINE; Free Full-Text Journals in Chemistry |
| subjects | Algorithms Amino Acid Sequence ATP-Binding Cassette Transporters - chemistry Bacterial Proteins - chemistry Bacterial Proteins - physiology Biological Transport Ion Channels - chemistry Ion Channels - physiology Membrane Proteins - chemistry Membrane Proteins - physiology Models, Molecular Models, Theoretical Peptide Fragments - chemistry Protein Conformation Protein Structure, Secondary |
| title | The Channel in Transporters is Formed by Residues That Are Rare in Transmembrane Helices |
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