{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/92991"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/92991","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"Investigating translational control of the ribosome using molecular dynamics simulations","abstract":"The ribosome is one of the most basic cellular machines and is ubiquitous in all living cells, responsible for the translation of genes into functional proteins. The central task of the ribosome is to promote peptide-bond transfer reaction by precisely aligning substrates of protein synthesis in ribosomal peptidyl-transferase center (PTC). To guarantee translation fidelity and cell survival, protein synthesis by the ribosome is tightly controlled by cofactors and a range of biological processes. In this thesis, we aim to investigate four translational control mechanisms that bring the ribosomal PTC into focus: (1) abolishment of ribosomal translation by the antibiotic action of macrolide drugs. (2) programmable translation arrest modulated by regulatory nascent peptides. (3) ribosomal discrimination of the chirality of amino acids within PTC. (4) translational control by EttA (energy-sensing translational throttle A) under energy-depleted cellular conditions. We employ computational approaches and collaborate closely with experimentalists. Our joint efforts advanced the understanding of translational control by the interplay of ribosome and cofactors. Our results may promote novel design of next generation antibiotic drugs because the bacterial ribosome is the main antibiotic drug target.","abstract_html":"The ribosome is one of the most basic cellular machines and is ubiquitous in all living cells, responsible for the translation of genes into functional proteins. The central task of the ribosome is to promote peptide-bond transfer reaction by precisely aligning substrates of protein synthesis in ribosomal peptidyl-transferase center (PTC). To guarantee translation fidelity and cell survival, protein synthesis by the ribosome is tightly controlled by cofactors and a range of biological processes. In this thesis, we aim to investigate four translational control mechanisms that bring the ribosomal PTC into focus: (1) abolishment of ribosomal translation by the antibiotic action of macrolide drugs. (2) programmable translation arrest modulated by regulatory nascent peptides. (3) ribosomal discrimination of the chirality of amino acids within PTC. (4) translational control by EttA (energy-sensing translational throttle A) under energy-depleted cellular conditions. We employ computational approaches and collaborate closely with experimentalists. Our joint efforts advanced the understanding of translational control by the interplay of ribosome and cofactors. Our results may promote novel design of next generation antibiotic drugs because the bacterial ribosome is the main antibiotic drug target.","abstract_has_math":false,"creators":["Liu, Bo"],"institution":"University of Illinois at Urbana-Champaign","degree_name":"Ph.D.","degree_level":"Dissertation","degree_discipline":"Biophysics & Computnl Biology","degree_department":null,"school":null,"contributors":["Schulten, Klaus","Jin, Hong","Luthey-Schulten, Zaida","Tajkhorshid, Emad"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2016,"date_issued":"2016-11-10T18:39:01Z","date_published":"2016-11-10T18:39:01Z","updated_at":"2026-07-22T22:26:35Z","subjects":["antibiotic","ribosome","molecular dynamics simulation","molecular dynamics flexible fitting","translation control"],"languages":["en"],"rights":["2016 by Bo Liu. 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(2) programmable translation arrest modulated by regulatory nascent peptides. (3) ribosomal discrimination of the chirality of amino acids within PTC. (4) translational control by EttA (energy-sensing translational throttle A) under energy-depleted cellular conditions. We employ computational approaches and collaborate closely with experimentalists. Our joint efforts advanced the understanding of translational control by the interplay of ribosome and cofactors. Our results may promote novel design of next generation antibiotic drugs because the bacterial ribosome is the main antibiotic drug target.","Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2018-08-01","The student, Bo Liu, accepted the attached license on 2016-05-12 at 18:27.","The student, Bo Liu, submitted this Dissertation for approval on 2016-05-12 at 18:45.","This Dissertation was approved for publication on 2016-05-16 at 15:18.","DSpace SAF Submission Ingestion Package generated from Vireo submission #9610 on 2016-11-10 at 12:24:11","Made available in DSpace on 2016-11-10T18:39:01Z (GMT). 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The central task of the ribosome is to promote peptide-bond transfer reaction by precisely aligning substrates of protein synthesis in ribosomal peptidyl-transferase center (PTC). To guarantee translation fidelity and cell survival, protein synthesis by the ribosome is tightly controlled by cofactors and a range of biological processes. In this thesis, we aim to investigate four translational control mechanisms that bring the ribosomal PTC into focus: (1) abolishment of ribosomal translation by the antibiotic action of macrolide drugs. (2) programmable translation arrest modulated by regulatory nascent peptides. (3) ribosomal discrimination of the chirality of amino acids within PTC. (4) translational control by EttA (energy-sensing translational throttle A) under energy-depleted cellular conditions. We employ computational approaches and collaborate closely with experimentalists. Our joint efforts advanced the understanding of translational control by the interplay of ribosome and cofactors. Our results may promote novel design of next generation antibiotic drugs because the bacterial ribosome is the main antibiotic drug target.","Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2018-08-01","The student, Bo Liu, accepted the attached license on 2016-05-12 at 18:27.","The student, Bo Liu, submitted this Dissertation for approval on 2016-05-12 at 18:45.","This Dissertation was approved for publication on 2016-05-16 at 15:18.","DSpace SAF Submission Ingestion Package generated from Vireo submission #9610 on 2016-11-10 at 12:24:11","Made available in DSpace on 2016-11-10T18:39:01Z (GMT). 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