Electrostatics in the Ribosomal Tunnel Modulate Chain Elongation Rates
Electrostatic potentials along the ribosomal exit tunnel are nonuniform and negative. The significance of electrostatics in the tunnel remains relatively uninvestigated, yet they are likely to play a role in translation and secondary folding of nascent peptides. To probe the role of nascent peptide...
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| Veröffentlicht in: | Journal of molecular biology 2008-12, Vol.384 (1), p.73-86 |
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| creator | Lu, Jianli Deutsch, Carol |
| description | Electrostatic potentials along the ribosomal exit tunnel are nonuniform and negative. The significance of electrostatics in the tunnel remains relatively uninvestigated, yet they are likely to play a role in translation and secondary folding of nascent peptides. To probe the role of nascent peptide charges in ribosome function, we used a molecular tape measure that was engineered to contain different numbers of charged amino acids localized to known regions of the tunnel and measured chain elongation rates. Positively charged arginine or lysine sequences produce transient arrest (pausing) before the nascent peptide is fully elongated. The rate of conversion from transiently arrested to full-length nascent peptide is faster for peptides containing neutral or negatively charged residues than for those containing positively charged residues. We provide experimental evidence that extraribosomal mechanisms do not account for this charge-specific pausing. We conclude that pausing is due to charge-specific interactions between the tunnel and the nascent peptide. |
| doi_str_mv | 10.1016/j.jmb.2008.08.089 |
| format | Article |
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The significance of electrostatics in the tunnel remains relatively uninvestigated, yet they are likely to play a role in translation and secondary folding of nascent peptides. To probe the role of nascent peptide charges in ribosome function, we used a molecular tape measure that was engineered to contain different numbers of charged amino acids localized to known regions of the tunnel and measured chain elongation rates. Positively charged arginine or lysine sequences produce transient arrest (pausing) before the nascent peptide is fully elongated. The rate of conversion from transiently arrested to full-length nascent peptide is faster for peptides containing neutral or negatively charged residues than for those containing positively charged residues. We provide experimental evidence that extraribosomal mechanisms do not account for this charge-specific pausing. We conclude that pausing is due to charge-specific interactions between the tunnel and the nascent peptide.</description><identifier>ISSN: 0022-2836</identifier><identifier>EISSN: 1089-8638</identifier><identifier>DOI: 10.1016/j.jmb.2008.08.089</identifier><identifier>PMID: 18822297</identifier><language>eng</language><publisher>England: Elsevier Ltd</publisher><subject>Amino Acid Sequence ; Amino Acid Substitution ; electrostatics ; Molecular Sequence Data ; nascent peptide ; Peptide Chain Elongation, Translational ; peptide elongation ; Peptides - chemistry ; Peptides - genetics ; Peptides - metabolism ; Potassium Channels, Voltage-Gated - chemistry ; Potassium Channels, Voltage-Gated - genetics ; Potassium Channels, Voltage-Gated - metabolism ; Ribosomes - chemistry ; Ribosomes - metabolism ; RNA, Messenger ; S4 transmembrane segment ; Static Electricity ; Thermodynamics ; Time Factors ; translation</subject><ispartof>Journal of molecular biology, 2008-12, Vol.384 (1), p.73-86</ispartof><rights>2008 Elsevier Ltd</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c546t-8898bd04ccefadfa8c02ec278d272d49f56d27e4b198b442563d0a794e24f7d13</citedby><cites>FETCH-LOGICAL-c546t-8898bd04ccefadfa8c02ec278d272d49f56d27e4b198b442563d0a794e24f7d13</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://www.sciencedirect.com/science/article/pii/S0022283608010991$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>230,314,776,780,881,3537,27901,27902,65306</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/18822297$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Lu, Jianli</creatorcontrib><creatorcontrib>Deutsch, Carol</creatorcontrib><title>Electrostatics in the Ribosomal Tunnel Modulate Chain Elongation Rates</title><title>Journal of molecular biology</title><addtitle>J Mol Biol</addtitle><description>Electrostatic potentials along the ribosomal exit tunnel are nonuniform and negative. The significance of electrostatics in the tunnel remains relatively uninvestigated, yet they are likely to play a role in translation and secondary folding of nascent peptides. To probe the role of nascent peptide charges in ribosome function, we used a molecular tape measure that was engineered to contain different numbers of charged amino acids localized to known regions of the tunnel and measured chain elongation rates. Positively charged arginine or lysine sequences produce transient arrest (pausing) before the nascent peptide is fully elongated. The rate of conversion from transiently arrested to full-length nascent peptide is faster for peptides containing neutral or negatively charged residues than for those containing positively charged residues. We provide experimental evidence that extraribosomal mechanisms do not account for this charge-specific pausing. We conclude that pausing is due to charge-specific interactions between the tunnel and the nascent peptide.</description><subject>Amino Acid Sequence</subject><subject>Amino Acid Substitution</subject><subject>electrostatics</subject><subject>Molecular Sequence Data</subject><subject>nascent peptide</subject><subject>Peptide Chain Elongation, Translational</subject><subject>peptide elongation</subject><subject>Peptides - chemistry</subject><subject>Peptides - genetics</subject><subject>Peptides - metabolism</subject><subject>Potassium Channels, Voltage-Gated - chemistry</subject><subject>Potassium Channels, Voltage-Gated - genetics</subject><subject>Potassium Channels, Voltage-Gated - metabolism</subject><subject>Ribosomes - chemistry</subject><subject>Ribosomes - metabolism</subject><subject>RNA, Messenger</subject><subject>S4 transmembrane segment</subject><subject>Static Electricity</subject><subject>Thermodynamics</subject><subject>Time Factors</subject><subject>translation</subject><issn>0022-2836</issn><issn>1089-8638</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2008</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkV1LwzAUhoMoOj9-gDfSK-86kzRtUwRBxvwARZB5HdLkdMtIE23agf_ezA0_bhQOnJA878vJeRE6JXhMMCkuluNlW48pxnz8WdUOGpHYUl5kfBeNMKY0pTwrDtBhCEuMcZ4xvo8OCOeU0qocoZupBdV3PvSyNyokxiX9ApJnU_vgW2mT2eAc2OTR68HKHpLJQkZmar2bR4V3yXO8Dcdor5E2wMm2H6GXm-lscpc-PN3eT64fUpWzok85r3itMVMKGqkbyRWmoGjJNS2pZlWTF_EErCaRY4zmRaaxLCsGlDWlJtkRutr4vg51C1qB6ztpxWtnWtm9Cy-N-P3izELM_UrQIs8pyaLB-dag828DhF60JiiwVjrwQxBFVdIyJ-W_IKlywjFfO5INqOIWQwfN1zQEi3VMYiliTGIdk_isKmrOfn7jW7HNJQKXGwDiMlcGOhGUAadAmy7mJbQ3f9h_AEa7pD8</recordid><startdate>20081205</startdate><enddate>20081205</enddate><creator>Lu, Jianli</creator><creator>Deutsch, Carol</creator><general>Elsevier Ltd</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>7TM</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20081205</creationdate><title>Electrostatics in the Ribosomal Tunnel Modulate Chain Elongation Rates</title><author>Lu, Jianli ; Deutsch, Carol</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c546t-8898bd04ccefadfa8c02ec278d272d49f56d27e4b198b442563d0a794e24f7d13</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2008</creationdate><topic>Amino Acid Sequence</topic><topic>Amino Acid Substitution</topic><topic>electrostatics</topic><topic>Molecular Sequence Data</topic><topic>nascent peptide</topic><topic>Peptide Chain Elongation, Translational</topic><topic>peptide elongation</topic><topic>Peptides - chemistry</topic><topic>Peptides - genetics</topic><topic>Peptides - metabolism</topic><topic>Potassium Channels, Voltage-Gated - chemistry</topic><topic>Potassium Channels, Voltage-Gated - genetics</topic><topic>Potassium Channels, Voltage-Gated - metabolism</topic><topic>Ribosomes - chemistry</topic><topic>Ribosomes - metabolism</topic><topic>RNA, Messenger</topic><topic>S4 transmembrane segment</topic><topic>Static Electricity</topic><topic>Thermodynamics</topic><topic>Time Factors</topic><topic>translation</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Lu, Jianli</creatorcontrib><creatorcontrib>Deutsch, Carol</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Nucleic Acids Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Journal of molecular biology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Lu, Jianli</au><au>Deutsch, Carol</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Electrostatics in the Ribosomal Tunnel Modulate Chain Elongation Rates</atitle><jtitle>Journal of molecular biology</jtitle><addtitle>J Mol Biol</addtitle><date>2008-12-05</date><risdate>2008</risdate><volume>384</volume><issue>1</issue><spage>73</spage><epage>86</epage><pages>73-86</pages><issn>0022-2836</issn><eissn>1089-8638</eissn><abstract>Electrostatic potentials along the ribosomal exit tunnel are nonuniform and negative. The significance of electrostatics in the tunnel remains relatively uninvestigated, yet they are likely to play a role in translation and secondary folding of nascent peptides. To probe the role of nascent peptide charges in ribosome function, we used a molecular tape measure that was engineered to contain different numbers of charged amino acids localized to known regions of the tunnel and measured chain elongation rates. Positively charged arginine or lysine sequences produce transient arrest (pausing) before the nascent peptide is fully elongated. The rate of conversion from transiently arrested to full-length nascent peptide is faster for peptides containing neutral or negatively charged residues than for those containing positively charged residues. We provide experimental evidence that extraribosomal mechanisms do not account for this charge-specific pausing. We conclude that pausing is due to charge-specific interactions between the tunnel and the nascent peptide.</abstract><cop>England</cop><pub>Elsevier Ltd</pub><pmid>18822297</pmid><doi>10.1016/j.jmb.2008.08.089</doi><tpages>14</tpages><oa>free_for_read</oa></addata></record> |
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| ispartof | Journal of molecular biology, 2008-12, Vol.384 (1), p.73-86 |
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| language | eng |
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| source | MEDLINE; Elsevier ScienceDirect Journals |
| subjects | Amino Acid Sequence Amino Acid Substitution electrostatics Molecular Sequence Data nascent peptide Peptide Chain Elongation, Translational peptide elongation Peptides - chemistry Peptides - genetics Peptides - metabolism Potassium Channels, Voltage-Gated - chemistry Potassium Channels, Voltage-Gated - genetics Potassium Channels, Voltage-Gated - metabolism Ribosomes - chemistry Ribosomes - metabolism RNA, Messenger S4 transmembrane segment Static Electricity Thermodynamics Time Factors translation |
| title | Electrostatics in the Ribosomal Tunnel Modulate Chain Elongation Rates |
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