Predicted calmodulin-binding sequence in the γ subunit of phosphorylase b kinase
A basic, amphiphilic α helix is a structural feature common to a variety of inhibitors of calmodulin and to the calmodulin‐binding domains of myosin light chain kinases. To aid in recognizing this structural feature in sequences of peptides and proteins we have developed a computer algorithm which s...
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| Veröffentlicht in: | Proteins, structure, function, and bioinformatics structure, function, and bioinformatics, 1987, Vol.2 (1), p.20-33 |
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| container_title | Proteins, structure, function, and bioinformatics |
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| creator | Degrado, William F. Erickson-Viitanen, Susan Wolfe Jr, Henry R. O'Neil, Karyn T. |
| description | A basic, amphiphilic α helix is a structural feature common to a variety of inhibitors of calmodulin and to the calmodulin‐binding domains of myosin light chain kinases. To aid in recognizing this structural feature in sequences of peptides and proteins we have developed a computer algorithm which searches for sequences of appropriate length, hydrophobicity, helical hydrophobic moment, and charge to be considered as potential calmodulin‐binding sequences. Such sequences occurred infrequently in proteins of known crystal structure. This algorithm was used to find the most likely site in the catalytic (γ) subunit of phosphorylase b kinase for interaction with calmodulin (the δ subunit). A peptide corresponding to this site (residues 341–361 of the γ subunit) was synthesized and found to bind calmodulin with approximately an 11 nM dissociation constant. A variant of this peptide in which an aspartic acid at position 7 in its sequence (347 of the γ subunit) was replaced with an asparagin was found to bind calmodulin with approximately a 3 nM dissociation constant. |
| doi_str_mv | 10.1002/prot.340020104 |
| format | Article |
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To aid in recognizing this structural feature in sequences of peptides and proteins we have developed a computer algorithm which searches for sequences of appropriate length, hydrophobicity, helical hydrophobic moment, and charge to be considered as potential calmodulin‐binding sequences. Such sequences occurred infrequently in proteins of known crystal structure. This algorithm was used to find the most likely site in the catalytic (γ) subunit of phosphorylase b kinase for interaction with calmodulin (the δ subunit). A peptide corresponding to this site (residues 341–361 of the γ subunit) was synthesized and found to bind calmodulin with approximately an 11 nM dissociation constant. A variant of this peptide in which an aspartic acid at position 7 in its sequence (347 of the γ subunit) was replaced with an asparagin was found to bind calmodulin with approximately a 3 nM dissociation constant.</description><identifier>ISSN: 0887-3585</identifier><identifier>EISSN: 1097-0134</identifier><identifier>DOI: 10.1002/prot.340020104</identifier><identifier>PMID: 3447166</identifier><identifier>CODEN: PSFGEY</identifier><language>eng</language><publisher>Hoboken: Wiley Subscription Services, Inc., A Wiley Company</publisher><subject>Algorithms ; Amino Acid Sequence ; Analytical, structural and metabolic biochemistry ; Binding Sites ; Binding, Competitive ; Biological and medical sciences ; calmodulin ; Calmodulin - metabolism ; calmodulin-binding peptide ; Circular Dichroism ; Enzymes and enzyme inhibitors ; Fundamental and applied biological sciences. Psychology ; helix ; hydrophobic moment ; In Vitro Techniques ; Models, Molecular ; Molecular Sequence Data ; peptide ; peptide design ; Peptide Fragments - metabolism ; phosphorylase kinase ; Phosphorylase Kinase - metabolism ; Protein Conformation ; Spectrometry, Fluorescence ; Transferases</subject><ispartof>Proteins, structure, function, and bioinformatics, 1987, Vol.2 (1), p.20-33</ispartof><rights>Copyright © 1987 Alan R. Liss, Inc.</rights><rights>1988 INIST-CNRS</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4384-c8fad3d8c11f0ffe34da1ad71bac965ec39a06e61e80b6437ef4c508705113403</citedby><cites>FETCH-LOGICAL-c4384-c8fad3d8c11f0ffe34da1ad71bac965ec39a06e61e80b6437ef4c508705113403</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1002%2Fprot.340020104$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1002%2Fprot.340020104$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,776,780,1411,4010,27900,27901,27902,45550,45551</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=7526169$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/3447166$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Degrado, William F.</creatorcontrib><creatorcontrib>Erickson-Viitanen, Susan</creatorcontrib><creatorcontrib>Wolfe Jr, Henry R.</creatorcontrib><creatorcontrib>O'Neil, Karyn T.</creatorcontrib><title>Predicted calmodulin-binding sequence in the γ subunit of phosphorylase b kinase</title><title>Proteins, structure, function, and bioinformatics</title><addtitle>Proteins</addtitle><description>A basic, amphiphilic α helix is a structural feature common to a variety of inhibitors of calmodulin and to the calmodulin‐binding domains of myosin light chain kinases. To aid in recognizing this structural feature in sequences of peptides and proteins we have developed a computer algorithm which searches for sequences of appropriate length, hydrophobicity, helical hydrophobic moment, and charge to be considered as potential calmodulin‐binding sequences. Such sequences occurred infrequently in proteins of known crystal structure. This algorithm was used to find the most likely site in the catalytic (γ) subunit of phosphorylase b kinase for interaction with calmodulin (the δ subunit). A peptide corresponding to this site (residues 341–361 of the γ subunit) was synthesized and found to bind calmodulin with approximately an 11 nM dissociation constant. A variant of this peptide in which an aspartic acid at position 7 in its sequence (347 of the γ subunit) was replaced with an asparagin was found to bind calmodulin with approximately a 3 nM dissociation constant.</description><subject>Algorithms</subject><subject>Amino Acid Sequence</subject><subject>Analytical, structural and metabolic biochemistry</subject><subject>Binding Sites</subject><subject>Binding, Competitive</subject><subject>Biological and medical sciences</subject><subject>calmodulin</subject><subject>Calmodulin - metabolism</subject><subject>calmodulin-binding peptide</subject><subject>Circular Dichroism</subject><subject>Enzymes and enzyme inhibitors</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>helix</subject><subject>hydrophobic moment</subject><subject>In Vitro Techniques</subject><subject>Models, Molecular</subject><subject>Molecular Sequence Data</subject><subject>peptide</subject><subject>peptide design</subject><subject>Peptide Fragments - metabolism</subject><subject>phosphorylase kinase</subject><subject>Phosphorylase Kinase - metabolism</subject><subject>Protein Conformation</subject><subject>Spectrometry, Fluorescence</subject><subject>Transferases</subject><issn>0887-3585</issn><issn>1097-0134</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>1987</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkc9u1DAQxi0EKtuFKzckHxC3LOPYsZ0jqmBBFFpQEdwsx55Q06yz2InoPhfvwTPhalcrbj1YM9J83_z5mZBnDFYMoH61TeO04qKkwEA8IAsGraqAcfGQLEBrVfFGN4_Jac4_AUC2XJ6QEy6EYlIuyOfLhD64CT11dtiMfh5CrLoQfYg_aMZfM0aHNEQ6XSP9-4fmuZtjmOjY0-31mMtLu8FmpB29CbEkT8ij3g4Znx7iknx9--bq7F11frF-f_b6vHKCa1E53VvPvXaM9dD3yIW3zHrFOuta2aDjrQWJkqGGTgqusBeuAa2gYeU44Evyct-3EChb5slsQnY4DDbiOGejVNuWI_W9QiZUU7d1XYSrvdClMeeEvdmmsLFpZxiYO9jmDrY5wi6G54fOc7dBf5Qf6Jb6i0Pd5kK3Tza6kI-yMlay8iFL0u5lv8OAu3uGmssvF1f_r1DtvSFPeHv02nRjpOKqMd8-rQ1fr-sP35uPhvN_lhqogA</recordid><startdate>1987</startdate><enddate>1987</enddate><creator>Degrado, William F.</creator><creator>Erickson-Viitanen, Susan</creator><creator>Wolfe Jr, Henry R.</creator><creator>O'Neil, Karyn T.</creator><general>Wiley Subscription Services, Inc., A Wiley Company</general><general>Wiley-Liss</general><scope>BSCLL</scope><scope>IQODW</scope><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>7QL</scope><scope>C1K</scope><scope>7X8</scope></search><sort><creationdate>1987</creationdate><title>Predicted calmodulin-binding sequence in the γ subunit of phosphorylase b kinase</title><author>Degrado, William F. ; Erickson-Viitanen, Susan ; Wolfe Jr, Henry R. ; O'Neil, Karyn T.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4384-c8fad3d8c11f0ffe34da1ad71bac965ec39a06e61e80b6437ef4c508705113403</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>1987</creationdate><topic>Algorithms</topic><topic>Amino Acid Sequence</topic><topic>Analytical, structural and metabolic biochemistry</topic><topic>Binding Sites</topic><topic>Binding, Competitive</topic><topic>Biological and medical sciences</topic><topic>calmodulin</topic><topic>Calmodulin - metabolism</topic><topic>calmodulin-binding peptide</topic><topic>Circular Dichroism</topic><topic>Enzymes and enzyme inhibitors</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>helix</topic><topic>hydrophobic moment</topic><topic>In Vitro Techniques</topic><topic>Models, Molecular</topic><topic>Molecular Sequence Data</topic><topic>peptide</topic><topic>peptide design</topic><topic>Peptide Fragments - metabolism</topic><topic>phosphorylase kinase</topic><topic>Phosphorylase Kinase - metabolism</topic><topic>Protein Conformation</topic><topic>Spectrometry, Fluorescence</topic><topic>Transferases</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Degrado, William F.</creatorcontrib><creatorcontrib>Erickson-Viitanen, Susan</creatorcontrib><creatorcontrib>Wolfe Jr, Henry R.</creatorcontrib><creatorcontrib>O'Neil, Karyn T.</creatorcontrib><collection>Istex</collection><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Environmental Sciences and Pollution Management</collection><collection>MEDLINE - Academic</collection><jtitle>Proteins, structure, function, and bioinformatics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Degrado, William F.</au><au>Erickson-Viitanen, Susan</au><au>Wolfe Jr, Henry R.</au><au>O'Neil, Karyn T.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Predicted calmodulin-binding sequence in the γ subunit of phosphorylase b kinase</atitle><jtitle>Proteins, structure, function, and bioinformatics</jtitle><addtitle>Proteins</addtitle><date>1987</date><risdate>1987</risdate><volume>2</volume><issue>1</issue><spage>20</spage><epage>33</epage><pages>20-33</pages><issn>0887-3585</issn><eissn>1097-0134</eissn><coden>PSFGEY</coden><abstract>A basic, amphiphilic α helix is a structural feature common to a variety of inhibitors of calmodulin and to the calmodulin‐binding domains of myosin light chain kinases. To aid in recognizing this structural feature in sequences of peptides and proteins we have developed a computer algorithm which searches for sequences of appropriate length, hydrophobicity, helical hydrophobic moment, and charge to be considered as potential calmodulin‐binding sequences. Such sequences occurred infrequently in proteins of known crystal structure. This algorithm was used to find the most likely site in the catalytic (γ) subunit of phosphorylase b kinase for interaction with calmodulin (the δ subunit). A peptide corresponding to this site (residues 341–361 of the γ subunit) was synthesized and found to bind calmodulin with approximately an 11 nM dissociation constant. A variant of this peptide in which an aspartic acid at position 7 in its sequence (347 of the γ subunit) was replaced with an asparagin was found to bind calmodulin with approximately a 3 nM dissociation constant.</abstract><cop>Hoboken</cop><pub>Wiley Subscription Services, Inc., A Wiley Company</pub><pmid>3447166</pmid><doi>10.1002/prot.340020104</doi><tpages>14</tpages></addata></record> |
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| ispartof | Proteins, structure, function, and bioinformatics, 1987, Vol.2 (1), p.20-33 |
| issn | 0887-3585 1097-0134 |
| language | eng |
| recordid | cdi_proquest_miscellaneous_77994718 |
| source | MEDLINE; Wiley Online Library Journals Frontfile Complete |
| subjects | Algorithms Amino Acid Sequence Analytical, structural and metabolic biochemistry Binding Sites Binding, Competitive Biological and medical sciences calmodulin Calmodulin - metabolism calmodulin-binding peptide Circular Dichroism Enzymes and enzyme inhibitors Fundamental and applied biological sciences. Psychology helix hydrophobic moment In Vitro Techniques Models, Molecular Molecular Sequence Data peptide peptide design Peptide Fragments - metabolism phosphorylase kinase Phosphorylase Kinase - metabolism Protein Conformation Spectrometry, Fluorescence Transferases |
| title | Predicted calmodulin-binding sequence in the γ subunit of phosphorylase b kinase |
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