{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,12]],"date-time":"2026-09-12T10:11:05Z","timestamp":1789207865204,"version":"build-2803163510"},"reference-count":55,"publisher":"American Chemical Society (ACS)","issue":"11","license":[{"start":{"date-parts":[[2015,9,8]],"date-time":"2015-09-08T00:00:00Z","timestamp":1441670400000},"content-version":"vor","delay-in-days":365,"URL":"https:\/\/pubs.acs.org\/page\/policy\/authorchoice_termsofuse.html"}],"funder":[{"DOI":"10.13039\/100000005","name":"U.S. Department of Defense","doi-asserted-by":"publisher","award":["NA"],"award-info":[{"award-number":["NA"]}],"id":[{"id":"10.13039\/100000005","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["R01GM093278"],"award-info":[{"award-number":["R01GM093278"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/na","name":"NASA Astrobiology Institute","doi-asserted-by":"publisher","award":["NNA09DA78A"],"award-info":[{"award-number":["NNA09DA78A"]}],"id":[{"id":"10.13039\/na","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,11,21]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Despite decades of research on the bacterial ribosome, the ribosomal exit tunnel is still poorly understood. Although it has been suggested that the exit tunnel is simply a convenient route of egress for the nascent chain, specific protein sequences serve to slow the rate of translation, suggesting some degree of interaction between the nascent peptide chain and the exit tunnel. To understand how the ribosome interacts with nascent peptide sequences, we synthesized and characterized a novel class of probe molecules. These peptide\u2013macrolide (or \u201cpeptolide\u201d) conjugates were designed to present unique peptide sequences to the exit tunnel. Biochemical and X-ray structural analyses of the interactions between these probes and the ribosome reveal interesting insights about the exit tunnel. Using translation inhibition and RNA structure probing assays, we find the exit tunnel has a relaxed preference for the directionality (N \u2192 C or C \u2192 N orientation) of the nascent peptides. Moreover, the X-ray crystal structure of one peptolide derived from a positively charged, reverse Nuclear Localization Sequence peptide, bound to the 70S bacterial ribosome, reveals that the macrolide ring of the peptolide binds in the same position as other macrolides. However, the peptide tail folds over the macrolide ring, oriented toward the peptidyl transferase center and interacting in a novel manner with 23S rRNA residue C2442 and His69 of ribosomal protein L4. These data suggest that these peptolides are viable probes for interrogating nascent peptide\u2013exit tunnel interaction.<\/jats:p>","DOI":"10.1021\/cb5003224","type":"journal-article","created":{"date-parts":[[2014,9,8]],"date-time":"2014-09-08T11:51:47Z","timestamp":1410177107000},"page":"2621-2631","source":"Crossref","is-referenced-by-count":8,"title":["Macrolide-Peptide Conjugates as Probes of the Path\nof Travel of the Nascent Peptides through the Ribosome"],"prefix":"10.1021","volume":"9","author":[{"given":"Arren Z.","family":"Washington","sequence":"first","affiliation":[{"name":"Georgia Institute of Technology , , , ,","place":["Atlanta, Georgia, United States, 30332-0400"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Derek B.","family":"Benicewicz","sequence":"additional","affiliation":[{"name":"Georgia Institute of Technology , , , ,","place":["Atlanta, Georgia, United States, 30332-0400"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joshua C.","family":"Canzoneri","sequence":"additional","affiliation":[{"name":"Georgia Institute of Technology , , , ,","place":["Atlanta, Georgia, United States, 30332-0400"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Crystal E.","family":"Fagan","sequence":"additional","affiliation":[{"name":"Emory University School of Medicine , , , ,","place":["Atlanta, Georgia, United States, 30322"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sandra C.","family":"Mwakwari","sequence":"additional","affiliation":[{"name":"Georgia Institute of Technology , , , ,","place":["Atlanta, Georgia, United States, 30332-0400"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tatsuya","family":"Maehigashi","sequence":"additional","affiliation":[{"name":"Emory University School of Medicine , , , ,","place":["Atlanta, Georgia, United States, 30322"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christine M.","family":"Dunham","sequence":"additional","affiliation":[{"name":"Emory University School of Medicine , , , ,","place":["Atlanta, Georgia, United States, 30322"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adegboyega K.","family":"Oyelere","sequence":"additional","affiliation":[{"name":"Georgia Institute of Technology , , , ,","place":["Atlanta, Georgia, United States, 30332-0400"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2014,9,8]]},"reference":[{"key":"2026090112501310600_cit1","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1038\/35030006","article-title":"Structure\nof the 30S ribosomal subunit","volume":"407","author":"Wimberly","year":"2000","journal-title":"Nature"},{"key":"2026090112501310600_cit2","doi-asserted-by":"crossref","first-page":"827","DOI":"10.1126\/science.1117230","article-title":"Structures of the bacterial ribosome\nat 3.5 \u00c5 resolution","volume":"310","author":"Schuwirth","year":"2005","journal-title":"Science"},{"key":"2026090112501310600_cit3","doi-asserted-by":"crossref","first-page":"1935","DOI":"10.1126\/science.1131127","article-title":"Structure\nof the 70S ribosome complexed with mRNA and tRNA","volume":"313","author":"Selmer","year":"2006","journal-title":"Science"},{"key":"2026090112501310600_cit4","doi-asserted-by":"crossref","first-page":"905","DOI":"10.1126\/science.289.5481.905","article-title":"The complete\natomic structure of the large ribosomal subunit at 2.4 A resolution","volume":"289","author":"Ban","year":"2000","journal-title":"Science"},{"key":"2026090112501310600_cit5","doi-asserted-by":"crossref","first-page":"920","DOI":"10.1126\/science.289.5481.920","article-title":"The structural\nbasis of ribosome activity in peptide bond formation","volume":"289","author":"Nissen","year":"2000","journal-title":"Science"},{"key":"2026090112501310600_cit6","doi-asserted-by":"crossref","first-page":"615","DOI":"10.1016\/S0092-8674(00)00084-2","article-title":"Structure of functionally activated\nsmall ribosomal subunit at 3.3 angstroms resolution","volume":"102","author":"Schluenzen","year":"2000","journal-title":"Cell"},{"key":"2026090112501310600_cit7","doi-asserted-by":"crossref","first-page":"893","DOI":"10.1016\/j.jmb.2006.05.023","article-title":"The geometry of\nthe ribosomal polypeptide exit tunnel","volume":"360","author":"Voss","year":"2006","journal-title":"J. Mol.\nBiol."},{"key":"2026090112501310600_cit8","doi-asserted-by":"crossref","first-page":"212","DOI":"10.1016\/S0959-440X(03)00034-4","article-title":"The chemistry of protein\nsynthesis and voyage through the ribosomal\ntunnel","volume":"13","author":"Jenni","year":"2003","journal-title":"Curr. Opin. Struct. Biol."},{"key":"2026090112501310600_cit9","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1016\/j.tibs.2005.11.007","article-title":"Nascent Peptide\nin the \u2018birth canal\u2019 of the ribosome","volume":"31","author":"Mankin","year":"2006","journal-title":"TRENDS Biochem. Sci."},{"key":"2026090112501310600_cit10","doi-asserted-by":"crossref","first-page":"160","DOI":"10.1016\/j.mib.2011.01.011","article-title":"Nascent polypeptide\nsequences that influence ribosome function","volume":"14","author":"Cruz-Vera","year":"2011","journal-title":"Curr. Opin. Micobiol."},{"key":"2026090112501310600_cit11","doi-asserted-by":"crossref","first-page":"331","DOI":"10.1016\/j.bpj.2012.06.005","article-title":"Mechanism\nof SecM-mediated stalling in the ribosome","volume":"103","author":"Gumbart","year":"2012","journal-title":"Biophys.\nJ."},{"key":"2026090112501310600_cit12","doi-asserted-by":"crossref","first-page":"190","DOI":"10.1016\/j.molcel.2008.02.026","article-title":"Molecular mechanism of drug-dependent\nribosome stalling","volume":"2","author":"Vazquez-Laslop","year":"2008","journal-title":"Mol. Cell"},{"key":"2026090112501310600_cit13","doi-asserted-by":"crossref","first-page":"1984","DOI":"10.1038\/ncomms2984","article-title":"Deregulation of\ntranslation due to post-transcriptional modification of rRNA explains\nwhy erm genes are inducible","volume":"4","author":"Gupta","year":"2013","journal-title":"Nat. Commun."},{"key":"2026090112501310600_cit14","doi-asserted-by":"crossref","first-page":"1412","DOI":"10.1126\/science.1177662","article-title":"Structural insight\ninto nascent polypeptide chain\u2013mediated translational stalling","volume":"326","author":"Seidelt","year":"2009","journal-title":"Science"},{"key":"2026090112501310600_cit15","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1016\/j.molcel.2006.05.021","article-title":"Translation arrest requires two-way\ncommunication between a nascent polypeptide and the ribosome","volume":"22","author":"Woolhead","year":"2006","journal-title":"Mol. Cell"},{"key":"2026090112501310600_cit16","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1016\/j.molcel.2009.04.002","article-title":"The plasticity\nof a translation arrest motif yields\ninsights into nascent polypeptide recognition inside the ribosome\ntunnel","volume":"34","author":"Yap","year":"2009","journal-title":"Mol. Cell"},{"key":"2026090112501310600_cit17","doi-asserted-by":"crossref","first-page":"3501","DOI":"10.1038\/ncomms4501","article-title":"Molecular basis for erythromycin-dependent ribosome\nstalling during translation of the ErmBL leader peptide","volume":"5","author":"Arenz","year":"2014","journal-title":"Nat. Commun."},{"key":"2026090112501310600_cit18","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1016\/j.molcel.2010.12.031","article-title":"Nascent peptide\nin the ribosome exit tunnel affects functional properties of the A-site\nof the peptidyl transferase center","volume":"41","author":"Ramu","year":"2011","journal-title":"Mol. Cell"},{"key":"2026090112501310600_cit19","doi-asserted-by":"crossref","first-page":"504","DOI":"10.1016\/j.chembiol.2010.04.008","article-title":"Interplay between\nthe ribosomal tunnel,\nnascent chain, and macrolides influences drug inhibition","volume":"17","author":"Starosta","year":"2010","journal-title":"Chem. Biol."},{"key":"2026090112501310600_cit20","doi-asserted-by":"publisher","first-page":"1861","DOI":"10.1021\/bc400236n","article-title":"Conjugates\nof amino acids and peptides with 5-O-mycaminosyltylonolide\nand their interaction with the ribosomal exit tunnel","volume":"24","author":"Shishkina","year":"2013","journal-title":"Bioconjugate Chem."},{"key":"2026090112501310600_cit21","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1111\/j.1749-6632.2011.06315.x","article-title":"Macrolide antibiotics\nin the ribosome exit tunnel:\nSpecies-specific binding and action","volume":"1241","author":"Kannan","year":"2011","journal-title":"Ann. N.Y.\nAcad. Sci."},{"key":"2026090112501310600_cit22","doi-asserted-by":"crossref","first-page":"17158","DOI":"10.1073\/pnas.1008685107","article-title":"Revisiting the structures\nof several antibiotics bound to the bacterial ribosome","volume":"107","author":"Bulkley","year":"2010","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2026090112501310600_cit23","doi-asserted-by":"crossref","first-page":"4276","DOI":"10.1128\/JB.185.14.4276-4279.2003","article-title":"Structural insight into the antibiotic\naction of telithromycin against resistant mutants","volume":"185","author":"Berisio","year":"2003","journal-title":"J. Bacteriol."},{"key":"2026090112501310600_cit24","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1016\/j.cell.2005.02.005","article-title":"Structures of MLSBK\nantibiotics bound to mutated large ribosomal subunits provide a structural\nexplanation for resistance","volume":"121","author":"Tu","year":"2005","journal-title":"Cell."},{"key":"2026090112501310600_cit25","doi-asserted-by":"crossref","first-page":"17152","DOI":"10.1073\/pnas.1007988107","article-title":"Structures of the Escherichia coli ribosome with antibiotics bound near the\npeptidyl transferase center explain spectra of drug action","volume":"107","author":"Dunkle","year":"2010","journal-title":"Proc. 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Chem."},{"issue":"8","key":"2026090112501310600_cit29","doi-asserted-by":"crossref","first-page":"664","DOI":"10.7164\/antibiotics.54.664","article-title":"Synthesis and antibacterial activity of the tricyclic\nketolides TE-802 and its analogs","volume":"54","author":"Kashimura","year":"2001","journal-title":"J. Antibiot."},{"key":"2026090112501310600_cit30","doi-asserted-by":"crossref","first-page":"4080","DOI":"10.1021\/jm980240d","article-title":"Synthesis\nand antibacterial activity of ketolides (6-O-methyl-3-oxoerythromycin\nderivatives): A new class of antibacterials highly potent against\nmacrolide-resistant and -susceptible respiratory pathogens","volume":"41","author":"Agouridas","year":"1998","journal-title":"J. Med. Chem."},{"key":"2026090112501310600_cit31a1","unstructured":"(a1)\n           Numerous\nexamples of Cu(I) catalyzed Huigsen cycloaddition\nreaction have appeared in the literature (a comprehensive list is\navailable at www.scripps.edu\/chem\/sharpless\/click.html (accessed\nApril 28, 2014)). Cited here are three examples:"},{"key":"2026090112501310600_cit31a","doi-asserted-by":"crossref","first-page":"2596","DOI":"10.1002\/1521-3773(20020715)41:14<2596::AID-ANIE2596>3.0.CO;2-4","article-title":"A stepwise\nhuigsen cycloaddition process: Copper (I)-catalyzed regioselective\n\u201cligation\u201d of azides and terminal alkynes","volume":"41","author":"Rostovtsev","year":"2002","journal-title":"Angew. Chem., Int. Ed."},{"key":"2026090112501310600_cit31b","doi-asserted-by":"crossref","first-page":"3057","DOI":"10.1021\/jo011148j","article-title":"Peptidotriazoles on solid phase:\n[1,2,3]- Triazoles by regiospecific copper(I)-catalyzed 1,3-dipolar\ncycloadditions of terminal alkynes to azides","volume":"67","author":"Tornoe","year":"2002","journal-title":"J. Org. Chem."},{"key":"2026090112501310600_cit31c","doi-asserted-by":"crossref","first-page":"2004","DOI":"10.1002\/1521-3773(20010601)40:11<2004::AID-ANIE2004>3.0.CO;2-5","article-title":"Click Chemistry: Diverse chemical function from a few\ngood reactions","volume":"40","author":"Kolb","year":"2001","journal-title":"Angw Chem., Int. Ed."},{"key":"2026090112501310600_cit32","doi-asserted-by":"crossref","first-page":"2739","DOI":"10.1016\/S0040-4039(00)99113-5","article-title":"Trialkylsilanes\nas scavengers for the trifluoroacetic acid deblocking of protecting\ngroups in peptide synthesis","volume":"30","author":"Pearson","year":"1989","journal-title":"Tetrahedron Lett."},{"key":"2026090112501310600_cit33","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1177\/1087057103260876","article-title":"A strategy for discovery\nof novel broad-spectrum antibacterials\nusing a high-throughput Streptococcus pneumoniae transcription\/translation\nscreen","volume":"9","author":"Pratt","year":"2004","journal-title":"J. Biomol Screen."},{"key":"2026090112501310600_cit34","doi-asserted-by":"crossref","first-page":"995","DOI":"10.1177\/1087057111416657","article-title":"A biochemical screen for identification\nof small-molecule regulators of the Wnt pathway using Xenopus egg\nextracts","volume":"16","author":"Thorne","year":"2011","journal-title":"J. Biomol. Scr."},{"key":"2026090112501310600_cit35","doi-asserted-by":"crossref","first-page":"2608","DOI":"10.1038\/nprot.2007.380","article-title":"DMS footprinting of\nstructured RNAs\nand RNA\u2013protein complexes","volume":"2","author":"Tijerina","year":"2010","journal-title":"Nat. Protoc."},{"key":"2026090112501310600_cit36","doi-asserted-by":"crossref","first-page":"21552","DOI":"10.1074\/jbc.270.37.21552","article-title":"Protein-induced\nfolding of a group I intron in cytochrome\nb pre-mRNA","volume":"270","author":"Shaw","year":"1995","journal-title":"J. Biol. Chem."},{"key":"2026090112501310600_cit37","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1128\/AAC.49.1.281-288.2005","article-title":"Binding site of\nthe bridged macrolides\nin the Escherichia coli ribosome","volume":"49","author":"Xiong","year":"2005","journal-title":"Antimicrob. Agents Chemother."},{"key":"2026090112501310600_cit38","doi-asserted-by":"crossref","first-page":"8900","DOI":"10.1073\/pnas.0401904101","article-title":"Visualization\nof ribosome-recycling factor on the Escherichia coli 70S ribosome: Functional implications","volume":"101","author":"Agrawal","year":"2004","journal-title":"Proc.\nNatl. Acad. Sci. U.S.A."},{"key":"2026090112501310600_cit39","first-page":"528","article-title":"Insights into\nsubstrate stabilization from snapshots of the peptidyl transferase\ncenter for the intact 70S ribosome","volume":"16","author":"Voorhees","year":"2009","journal-title":"NSMB"},{"key":"2026090112501310600_cit40","doi-asserted-by":"crossref","first-page":"1203","DOI":"10.1126\/science.1194294","article-title":"Crystal structure of\nthe eukaryotic ribosome","volume":"330","author":"Ben-Shem","year":"2010","journal-title":"Science."},{"key":"2026090112501310600_cit41","unstructured":"http:\/\/apollo.chemistry.gatech.edu\/RiboVision\/ (accessed Dec.\n2, 2013)."},{"key":"2026090112501310600_cit42","doi-asserted-by":"crossref","first-page":"1194","DOI":"10.1096\/fj.05-5231fje","article-title":"Identification and characterization\nof riproximin,\na new type II ribosome-inactivating protein with antineoplastic activity\nfrom Ximenia americana","volume":"20","author":"Voss","year":"2006","journal-title":"FASEB\nJ."},{"key":"2026090112501310600_cit43","doi-asserted-by":"crossref","first-page":"274","DOI":"10.1016\/j.sbi.2011.01.007","article-title":"The ribosomal tunnel\nas a functional environment for\nnascent polypeptide folding and translational stalling","volume":"21","author":"Wilson","year":"2011","journal-title":"Curr. 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Commun."},{"key":"2026090112501310600_cit45","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1093\/oso\/9780199636518.003.0010","article-title":"Footprinting and modification-interference analysis of binding sites\non RNA","volume-title":"RNA:Protein Interactions, A Practical\nApproach","author":"Merryman","year":"1998"},{"key":"2026090112501310600_cit46","doi-asserted-by":"crossref","first-page":"3207","DOI":"10.1016\/j.febslet.2005.03.023","article-title":"A crevice adjoining\nthe ribosome tunnel: Hints for\ncotranslational folding","volume":"579","author":"Amit","year":"2005","journal-title":"FEBS Lett."},{"key":"2026090112501310600_cit47","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1107\/S0907444909047337","article-title":"XDS","volume":"66","author":"Kabsch","year":"2010","journal-title":"Acta Crystallogr.,\nSect. D: Biol. Crystallogr."},{"key":"2026090112501310600_cit48","doi-asserted-by":"crossref","first-page":"391","DOI":"10.1107\/S0907444912001308","article-title":"Towards automated crystallographic\nstructure refinement with phenix.refine","volume":"68","author":"Afonine","year":"2012","journal-title":"Acta\nCryst. D"},{"key":"2026090112501310600_cit49","doi-asserted-by":"crossref","first-page":"486","DOI":"10.1107\/S0907444910007493","article-title":"Features and development\nof Coot","volume":"66","author":"Emsley","year":"2010","journal-title":"Acta Crystallogr.,\nSect. D: Biol. Crystallogr."},{"key":"2026090112501310600_cit50","unstructured":"The\nPyMOL Molecular Graphics System, Version 1.5.0.4 Schro\u0308dinger, LLC: New York."},{"key":"2026090112501310600_cit51","doi-asserted-by":"crossref","first-page":"1821","DOI":"10.1039\/b902338k","article-title":"High-throughput synthesis\nof azide libraries suitable for direct\nchemistry and in situ screening","volume":"7","author":"Stinivasan","year":"2009","journal-title":"Org. Biomol. Chem."},{"key":"2026090112501310600_cit52","doi-asserted-by":"crossref","first-page":"20665","DOI":"10.1073\/pnas.0810826105","article-title":"Structural basis for cross-resistance\nto ribosomal PTC antibiotics","volume":"105","author":"Davidovich","year":"2008","journal-title":"Proc. Natl. Acad.\nSci. U.S.A."}],"container-title":["ACS Chemical Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/cb5003224","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/acbcct\/article-pdf\/9\/11\/2621\/15709148\/cb5003224.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pubs.acs.org\/acbcct\/article-pdf\/9\/11\/2621\/15709148\/cb5003224.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T16:50:26Z","timestamp":1788281426000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/acbcct\/article\/9\/11\/2621\/1477979\/Macrolide-Peptide-Conjugates-as-Probes-of-the-Path"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,9,8]]},"references-count":55,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2014,9,8]]},"published-print":{"date-parts":[[2014,11,21]]}},"URL":"https:\/\/doi.org\/10.1021\/cb5003224","relation":{},"ISSN":["1554-8929","1554-8937"],"issn-type":[{"value":"1554-8929","type":"print"},{"value":"1554-8937","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,9,8]]}}}