Protein Sentezi (Translasyon Mekanizması)

Sabatini DD, Tashiro Y, Palade GE. On the attachment of ribosomes to microsomal membranes. Journal of Molecular Biology (JMB); 1966; 19, 503-IN9. doi:10.1016/S0022-2836(66)80019-0

Frank J. The mechanism of translation. F1000Research; 2017; 6, 198. doi:10.12688/f1000research.9760.1

Tavernarakis N. Ageing and the regulation of protein synthesis: a balancing act? Trends in Cell Biology; 2008;18(5):228-235. doi: 10.1016/j.tcb.2008.02.004.

Rodnina MV, Wintermeyer W. Fidelity of Aminoacyl-tRNA Selection on the Ribosome: Kinetic and Structural Mechanisms. Annual Review of Biochemistry; 2001;70:415–435. doi: 10.1146/annurev.biochem.70.1.415

https://www.mlsu.ac.in/econtents/91_Complete%20Translation.pdf Clancy S, Brown W. (2008) Translation: DNA to mRNA to

Protein. Nature Education; 2008; 1(1):101.

https://bio.libretexts.org/Courses/University_of_California_Davis/BIS_2A%3A_Introductory_Biology_(Easlon)/Readings/19.1%3A_TranslationProtein_Synthesis

Frank J. The mechanism of translation. F1000Research; 2017; 6: 198. doi:10.12688/f1000research.9760.1

Turowski TW, Tollervey D. Transcription by RNA polymerase III: insights into mechanism and regulation. Biochemical Society Transactions; 2016; 44 (5): 1367–1375.

http://www2.csudh.edu/nsturm/CHEMXL153/ProteinSynthesisMaturation.htm

http://www.bx.psu.edu/~ross/workmg/TranslationCh14.htm

Bock LV, Kolář MH, Grubmüller H. Molecular simulations of the ribosome and associated translation factors. Current Opinion in Structural Biology (COSB); 2018;49:27–35. doi:10.1016/j.sbi.2017.11.003

Hinnebusch AG. The Scanning Mechanism of Eukaryotic Translation Initiation. Annual Review of Biochemistry; 2014;83:779–812. doi:10.1146/annurev-biochem-060713-035802

Rodnina MV, Wintermeyer W. Fidelity of Aminoacyl-tRNA Selection on the Ribosome: Kinetic and Structural Mechanisms. Annual Review of Biochemistry; 2001;70:415–435. doi:10.1146/annurev.biochem.70.1.415

Hinnebusch AG, Lorsch JR. The Mechanism of Eukaryotic Translation Initiation: New Insights and Challenges. Cold Spring Harbor Perspectives in Biology; 2012;4:a011544–a011544. doi:10.1101/cshperspect.a011544

Kolitz SE, Takacs JE, Lorsch JR. Kinetic and thermodynamic analysis of the role of start codon/anticodon base pairing during eukaryotic translation initiation. RNA; 2009;15: 138–152. doi:10.1261/rna.1318509

Lomakin IB, Shirokikh NE, Yusupov MM, et al. 2006. The fidelity of translation initiation: reciprocal activities of eIF1, IF3 and YciH. EMBO Journal; 2006;25:196–210. doi:10.1038/sj.emboj.7600904

Gutierrez E, Shin BS Woolstenhulme CJ, et al. eIF5A Promotes Translation of Polyproline Motifs. Molecular Cell; 2013; 51(1): 35–45. doi: 10.1016/j.molcel.2013.04.021

Cooper GM and Hausman RE. The Cell: A Molecular Approach. Third Edition., 3rd ed. ASM Press / Sinauer Associates, Washington DC, USA; 2004.

20. https://www.genome.gov/genetics-glossary/Base-Pair

Chezhiyan JE. A Review on Protein Synthesis and Genetic Code. Biochemistry & Molecular Biology Journal; 2021;7 (1):1-5.

Solak M, Şengil AZ, Öztaş S. Rekombinant DNA Teknolojisi Temel İlkeleri ve Uygulama Alanları. Bilim Teknik Kitabevi, Manisa: 1997, ss 27-35.

Alberts B, Bray D, Lewis J, et al. In: Molecular biology of the cell. 3rd ed. New York: Garland: 1994. p. 655–720. 48.

DiMauro S, Wallace DC. Mitochondria/ DNA in humanpathology. Raven Press, New York: 1993. pp 1-172.

Öztaş S, Yakan B. Mitochondrial DNA and related diseases. Erciyes Tıp Dergisi (Erciyes Medical Journal): 199;21(1): 63-71.

https://tr.khanacademy.org/science/biology/gene-expression-central-dogma/translation-polypeptides/a/translation-overview

Sanders M, Bowman J. Genetic Analysis: An Integrated Approach (Masteringgenetics) 3rd Edition. Publisher Pearson: 2021.

https://www.nature.com/scitable/topicpage/protein-structure-14122136/

Bruce A, Alexander J, Julian L, et al. Molecular Biology of the Cell, 4 th. ed. Garland Science, New York: 2022.

LaPelusa A, Kaushik R. In: StatPearls [Internet]. Physiology, ProteinsTreasure Island (FL): StatPearls Publishing; 2022.

Mignone F, Gissi C, Liuni S, et al.. Untranslated regions of mRNAs Genome Biology; 2002;3 (3): REVIEWS0004. doi:10.1186/gb-2002-3-3-reviews0004

Wen JD, Kuo ST, David Chou HH. The diversity of Shine-Dalgarno sequences sheds light on the evolution of translation initiation. RNA Biology; 2021; 18(11): 1489–1500. 10.1080/15476286.2020.1861406

Jackson RJ, Hellen CUT, Pestova TV. The mechanısm of eukaryotıc translatıon ınıtıatıon and prıncıples of ıts regulatıon. Nature Reviews Molecular Cell Biology; 2010; 11(2): 113–127. doi:10.1038/nrm2838

Kapp LD, Lorsch JR. The Molecular Mechanics of Eukaryotic Translation. Annual Review of Biochemistry; 2004;73:657–704. doi:10.1146/annurev.biochem.73.030403.080419

Asano K, Clayton J, Shalev A, etal. 2000. A multifactor complex of eukaryotic initiation factors, eIF1, eIF2, eIF3, eIF5, and initiator tRNA Met is an important translation initiation intermediate in vivo. Genes & Development; 2000;14:2534–2546. doi:10.1101/gad.831800

Dennis MD, Person MD, Browning KS. Phosphorylation of Plant Translation Initiation Factors by CK2 Enhances the in Vitro Interaction of Multifactor Complex Components. Journal of Biological Chemistry (JBC); 2009; 284: 20615–20628. doi:10.1074/jbc.M109.007658

Sokabe M, Fraser CS, Hershey JWB. The human translation initiation multi-factor complex promotes methionyl-tRNA i binding to the 40S ribosomal subunit. Nucleic Acids Research; 2012; 40, 905–913. doi:10.1093/nar/gkr772

https://www.pearson.com/content/dam/one-dot-com/one-dot-com/us/en/higher-ed/en/products-services/sanders-2e-info/pdf/ch9.pdf

Jackson RJ, Hellen CUT, Pestova TV. The mechanism of eukaryotic translation initiation and principles of its regulation. Nature Reviews Molecular Cell Biology; 2010;11:113–127. doi:10.1038/nrm2838

Antoun A, Pavlov MY, Lovmar M, et al. How initiation factors tune the rate of initiation of protein synthesis in bacteria. EMBO Journal; 2006;25(11):2539–2550.

Clark DP, Pazdernik NJ, McGehee MR. Chapter 13 - Protein Synthesis. Molecular Biology (Third Edition): 2019, Pages 397-444.

Saito K, Green R, Buskirk AR. Translational initiation in E. coli occurs at the correct sites genome-wide in the absence of mRNA-rRNA base-pairing. ELife; 2020;9:e55002. doi:10.7554/eLife.55002

Sacerdot C, Fayat G, Dessen P, et al. Sequence of a 1.26-kb DNA fragment containing the structural gene for E.coli initiation factor IF3: presence of an AUU initiator codon. EMBO Journal; 1982; 1: 311–315. doi:10.1002/j.1460-2075.1982.tb01166.x

Kozak M. Comparison of initiation of protein synthesis in procaryotes, eucaryotes, and organelles. Microbiological Reviews; 1983; 47: 1–45. doi:10.1128/mr.47.1.1-45.1983

Marshall RA, Aitken CE, Puglisi JD. GTP hydrolysis by IF2 guides progression of the ribosome into elongation. Molecular Cell. 2009; 35(1): 37–47. doi:10.1016/j.molcel.2009.06.008

Frank J, Gao H, Sengupta J, et al. The process of mRNA-tRNA translocation. Proceedings of the National Academy of Sciences (PNAS); 2007;104(50):19671-8. doi:10.1073/pnas.0708517104

Harvey KL, Jarocki VM, Charles IG, et al. The Diverse Functional Roles of Elongation Factor Tu (EF-Tu) in Microbial Pathogenesis. Frontiers in Microbiology; 2019;10:2351. doi: 10.3389/fmicb.2019.02351. eCollection 2019.

Xu B, Liu L, Song G. Functions and Regulation of Translation Elongation Factors. Frontiers in Molecular Biosciences; 2022;8:816398.

https://www.studocu.com/in/document/university-of-delhi/zoology/40632-ch08-rev151-188-protein-synthesis/31674839

Lipmann F. Polypeptide chain elongation in protein biosynthesis Science.1969;164(3883):1024-31. doi:10.1126/science.164.3883.1024.

Vesper O, Knud H. Nierhaus, Translation Elongation in Bacteria in Encyclopedia of Biological Chemistry; 2004.

Alexander S. Spirin. Elongation Cycle, Step III: Translocation. Ribosomes; 1999; pp 213–239.

Brenner S, Stretton AO, Kaplan S (1965) Genetic code: the ‘nonsense' triplets for chain termination and their suppression. Nature; 1965; 206: 994–998. doi:10.1038/206994a0

Arkov AL. 1998. Mutations in RNAs of both ribosomal subunits cause defects in translation termination. EMBO Journal; 1998; 17, 1507–1514. doi:10.1093/emboj/17.5.1507

Caskey CT, Beaudet AL, Scolnick EM, et al. Hydrolysis of fMet-tRNA by Peptidyl Transferase. Proceedings of the National Academy of Sciences (PNAS); 1971; 68, 3163–3167. doi:10.1073/pnas.68.12.3163

Zavialov AV, Mora L, Buckingham RH, et al. Release of Peptide Promoted by the GGQ Motif of Class 1 Release Factors Regulates the GTPase Activity of RF3. Molecular Cell; 2002;10;789–798. doi:10.1016/S1097-2765(02)00691-3

Frolova L, Le Goff X, Rasmussen HH, et al. A highly conserved eukaryotic protein family possessing properties of polypeptide chain release factor. Nature; 1994;372:701–703. doi:10.1038/372701a0

Kisselev L. 2003. NEW EMBO MEMBER’S REVIEW: Termination of translation: interplay of mRNA, rRNAs and release factors? EMBO Journal; 2003;22:175–182. doi:10.1093/emboj/cdg017

Tuite MF, Stansfield I. Termination of protein synthesis. Molecular Biology Reports; 1994;19:171–181. doi:10.1007/BF00986959

Zhouravleva, G, Frolova L, Le Goff X, et al. Termination of translation in eukaryotes is governed by two interacting polypeptide chain release factors, eRF1 and eRF3. EMBO Journal; 1995; 14:4065–4072. doi:10.1002/j.1460-2075.1995.tb00078.x

Frolova L, Le Goff X, Zhouravleva G, et al. Eukaryotic polypeptide chain release factor eRF3 is an eRF1- and ribosome-dependent guanosine triphosphatase. RNA; 1996; 2, 334–41.

Haro I, Sanmartí R, Gómara MJ. Implications of Post-TranslationalModifications in Autoimmunity with Emphasis on Citrullination, Homocitrullination and Acetylation for the Pathogenesis, Diagnosis and Prognosis of Rheumatoid Arthritis. International Journal of Molecular Sciences; 2022; 23:15803.

Pieroni S, Castelli M, Piobbico D, et al. The Four Homeostasis Knights: In Balance upon Post-Translational Modifications. International Journal of Molecular Sciences; 2022; 23: 14480.

Sabatini DD, Tashiro Y, Palade GE. On the attachment of ribosomes to microsomal membranes. Journal of Molecular Biology (JMB); 1966; 19, 503-IN9. doi:10.1016/S0022-2836(66)80019-0

Frank J. The mechanism of translation. F1000Research; 2017; 6, 198. doi:10.12688/f1000research.9760.1

Tavernarakis N. Ageing and the regulation of protein synthesis: a balancing act? Trends in Cell Biology; 2008;18(5):228-235. doi: 10.1016/j.tcb.2008.02.004.

Rodnina MV, Wintermeyer W. Fidelity of Aminoacyl-tRNA Selection on the Ribosome: Kinetic and Structural Mechanisms. Annual Review of Biochemistry; 2001;70:415–435. doi: 10.1146/annurev.biochem.70.1.415

https://www.mlsu.ac.in/econtents/91_Complete%20Translation.pdf Clancy S, Brown W. (2008) Translation: DNA to mRNA to

Protein. Nature Education; 2008; 1(1):101.

https://bio.libretexts.org/Courses/University_of_California_Davis/BIS_2A%3A_Introductory_Biology_(Easlon)/Readings/19.1%3A_TranslationProtein_Synthesis

Frank J. The mechanism of translation. F1000Research; 2017; 6: 198. doi:10.12688/f1000research.9760.1

Turowski TW, Tollervey D. Transcription by RNA polymerase III: insights into mechanism and regulation. Biochemical Society Transactions; 2016; 44 (5): 1367–1375.

http://www2.csudh.edu/nsturm/CHEMXL153/ProteinSynthesisMaturation.htm

http://www.bx.psu.edu/~ross/workmg/TranslationCh14.htm

Bock LV, Kolář MH, Grubmüller H. Molecular simulations of the ribosome and associated translation factors. Current Opinion in Structural Biology (COSB); 2018;49:27–35. doi:10.1016/j.sbi.2017.11.003

Hinnebusch AG. The Scanning Mechanism of Eukaryotic Translation Initiation. Annual Review of Biochemistry; 2014;83:779–812. doi:10.1146/annurev-biochem-060713-035802

Rodnina MV, Wintermeyer W. Fidelity of Aminoacyl-tRNA Selection on the Ribosome: Kinetic and Structural Mechanisms. Annual Review of Biochemistry; 2001;70:415–435. doi:10.1146/annurev.biochem.70.1.415

Hinnebusch AG, Lorsch JR. The Mechanism of Eukaryotic Translation Initiation: New Insights and Challenges. Cold Spring Harbor Perspectives in Biology; 2012;4:a011544–a011544. doi:10.1101/cshperspect.a011544

Kolitz SE, Takacs JE, Lorsch JR. Kinetic and thermodynamic analysis of the role of start codon/anticodon base pairing during eukaryotic translation initiation. RNA; 2009;15: 138–152. doi:10.1261/rna.1318509

Lomakin IB, Shirokikh NE, Yusupov MM, et al. 2006. The fidelity of translation initiation: reciprocal activities of eIF1, IF3 and YciH. EMBO Journal; 2006;25:196–210. doi:10.1038/sj.emboj.7600904

Gutierrez E, Shin BS Woolstenhulme CJ, et al. eIF5A Promotes Translation of Polyproline Motifs. Molecular Cell; 2013; 51(1): 35–45. doi: 10.1016/j.molcel.2013.04.021

Cooper GM and Hausman RE. The Cell: A Molecular Approach. Third Edition., 3rd ed. ASM Press / Sinauer Associates, Washington DC, USA; 2004.

20. https://www.genome.gov/genetics-glossary/Base-Pair

Chezhiyan JE. A Review on Protein Synthesis and Genetic Code. Biochemistry & Molecular Biology Journal; 2021;7 (1):1-5.

Solak M, Şengil AZ, Öztaş S. Rekombinant DNA Teknolojisi Temel İlkeleri ve Uygulama Alanları. Bilim Teknik Kitabevi, Manisa: 1997, ss 27-35.

Alberts B, Bray D, Lewis J, et al. In: Molecular biology of the cell. 3rd ed. New York: Garland: 1994. p. 655–720. 48.

DiMauro S, Wallace DC. Mitochondria/ DNA in humanpathology. Raven Press, New York: 1993. pp 1-172.

Öztaş S, Yakan B. Mitochondrial DNA and related diseases. Erciyes Tıp Dergisi (Erciyes Medical Journal): 199;21(1): 63-71.

https://tr.khanacademy.org/science/biology/gene-expression-central-dogma/translation-polypeptides/a/translation-overview

Sanders M, Bowman J. Genetic Analysis: An Integrated Approach (Masteringgenetics) 3rd Edition. Publisher Pearson: 2021.

https://www.nature.com/scitable/topicpage/protein-structure-14122136/

Bruce A, Alexander J, Julian L, et al. Molecular Biology of the Cell, 4 th. ed. Garland Science, New York: 2022.

LaPelusa A, Kaushik R. In: StatPearls [Internet]. Physiology, ProteinsTreasure Island (FL): StatPearls Publishing; 2022.

Mignone F, Gissi C, Liuni S, et al.. Untranslated regions of mRNAs Genome Biology; 2002;3 (3): REVIEWS0004. doi:10.1186/gb-2002-3-3-reviews0004

Wen JD, Kuo ST, David Chou HH. The diversity of Shine-Dalgarno sequences sheds light on the evolution of translation initiation. RNA Biology; 2021; 18(11): 1489–1500. 10.1080/15476286.2020.1861406

Jackson RJ, Hellen CUT, Pestova TV. The mechanısm of eukaryotıc translatıon ınıtıatıon and prıncıples of ıts regulatıon. Nature Reviews Molecular Cell Biology; 2010; 11(2): 113–127. doi:10.1038/nrm2838

Kapp LD, Lorsch JR. The Molecular Mechanics of Eukaryotic Translation. Annual Review of Biochemistry; 2004;73:657–704. doi:10.1146/annurev.biochem.73.030403.080419

Asano K, Clayton J, Shalev A, etal. 2000. A multifactor complex of eukaryotic initiation factors, eIF1, eIF2, eIF3, eIF5, and initiator tRNA Met is an important translation initiation intermediate in vivo. Genes & Development; 2000;14:2534–2546. doi:10.1101/gad.831800

Dennis MD, Person MD, Browning KS. Phosphorylation of Plant Translation Initiation Factors by CK2 Enhances the in Vitro Interaction of Multifactor Complex Components. Journal of Biological Chemistry (JBC); 2009; 284: 20615–20628. doi:10.1074/jbc.M109.007658

Sokabe M, Fraser CS, Hershey JWB. The human translation initiation multi-factor complex promotes methionyl-tRNA i binding to the 40S ribosomal subunit. Nucleic Acids Research; 2012; 40, 905–913. doi:10.1093/nar/gkr772

https://www.pearson.com/content/dam/one-dot-com/one-dot-com/us/en/higher-ed/en/products-services/sanders-2e-info/pdf/ch9.pdf

Jackson RJ, Hellen CUT, Pestova TV. The mechanism of eukaryotic translation initiation and principles of its regulation. Nature Reviews Molecular Cell Biology; 2010;11:113–127. doi:10.1038/nrm2838

Antoun A, Pavlov MY, Lovmar M, et al. How initiation factors tune the rate of initiation of protein synthesis in bacteria. EMBO Journal; 2006;25(11):2539–2550.

Clark DP, Pazdernik NJ, McGehee MR. Chapter 13 - Protein Synthesis. Molecular Biology (Third Edition): 2019, Pages 397-444.

Saito K, Green R, Buskirk AR. Translational initiation in E. coli occurs at the correct sites genome-wide in the absence of mRNA-rRNA base-pairing. ELife; 2020;9:e55002. doi:10.7554/eLife.55002

Sacerdot C, Fayat G, Dessen P, et al. Sequence of a 1.26-kb DNA fragment containing the structural gene for E.coli initiation factor IF3: presence of an AUU initiator codon. EMBO Journal; 1982; 1: 311–315. doi:10.1002/j.1460-2075.1982.tb01166.x

Kozak M. Comparison of initiation of protein synthesis in procaryotes, eucaryotes, and organelles. Microbiological Reviews; 1983; 47: 1–45. doi:10.1128/mr.47.1.1-45.1983

Marshall RA, Aitken CE, Puglisi JD. GTP hydrolysis by IF2 guides progression of the ribosome into elongation. Molecular Cell. 2009; 35(1): 37–47. doi:10.1016/j.molcel.2009.06.008

Frank J, Gao H, Sengupta J, et al. The process of mRNA-tRNA translocation. Proceedings of the National Academy of Sciences (PNAS); 2007;104(50):19671-8. doi:10.1073/pnas.0708517104

Harvey KL, Jarocki VM, Charles IG, et al. The Diverse Functional Roles of Elongation Factor Tu (EF-Tu) in Microbial Pathogenesis. Frontiers in Microbiology; 2019;10:2351. doi: 10.3389/fmicb.2019.02351. eCollection 2019.

Xu B, Liu L, Song G. Functions and Regulation of Translation Elongation Factors. Frontiers in Molecular Biosciences; 2022;8:816398.

https://www.studocu.com/in/document/university-of-delhi/zoology/40632-ch08-rev151-188-protein-synthesis/31674839

Lipmann F. Polypeptide chain elongation in protein biosynthesis Science.1969;164(3883):1024-31. doi:10.1126/science.164.3883.1024.

Vesper O, Knud H. Nierhaus, Translation Elongation in Bacteria in Encyclopedia of Biological Chemistry; 2004.

Alexander S. Spirin. Elongation Cycle, Step III: Translocation. Ribosomes; 1999; pp 213–239.

Brenner S, Stretton AO, Kaplan S (1965) Genetic code: the ‘nonsense' triplets for chain termination and their suppression. Nature; 1965; 206: 994–998. doi:10.1038/206994a0

Arkov AL. 1998. Mutations in RNAs of both ribosomal subunits cause defects in translation termination. EMBO Journal; 1998; 17, 1507–1514. doi:10.1093/emboj/17.5.1507

Caskey CT, Beaudet AL, Scolnick EM, et al. Hydrolysis of fMet-tRNA by Peptidyl Transferase. Proceedings of the National Academy of Sciences (PNAS); 1971; 68, 3163–3167. doi:10.1073/pnas.68.12.3163

Zavialov AV, Mora L, Buckingham RH, et al. Release of Peptide Promoted by the GGQ Motif of Class 1 Release Factors Regulates the GTPase Activity of RF3. Molecular Cell; 2002;10;789–798. doi:10.1016/S1097-2765(02)00691-3

Frolova L, Le Goff X, Rasmussen HH, et al. A highly conserved eukaryotic protein family possessing properties of polypeptide chain release factor. Nature; 1994;372:701–703. doi:10.1038/372701a0

Kisselev L. 2003. NEW EMBO MEMBER’S REVIEW: Termination of translation: interplay of mRNA, rRNAs and release factors? EMBO Journal; 2003;22:175–182. doi:10.1093/emboj/cdg017

Tuite MF, Stansfield I. Termination of protein synthesis. Molecular Biology Reports; 1994;19:171–181. doi:10.1007/BF00986959

Zhouravleva, G, Frolova L, Le Goff X, et al. Termination of translation in eukaryotes is governed by two interacting polypeptide chain release factors, eRF1 and eRF3. EMBO Journal; 1995; 14:4065–4072. doi:10.1002/j.1460-2075.1995.tb00078.x

Frolova L, Le Goff X, Zhouravleva G, et al. Eukaryotic polypeptide chain release factor eRF3 is an eRF1- and ribosome-dependent guanosine triphosphatase. RNA; 1996; 2, 334–41.

Haro I, Sanmartí R, Gómara MJ. Implications of Post-TranslationalModifications in Autoimmunity with Emphasis on Citrullination, Homocitrullination and Acetylation for the Pathogenesis, Diagnosis and Prognosis of Rheumatoid Arthritis. International Journal of Molecular Sciences; 2022; 23:15803.

Pieroni S, Castelli M, Piobbico D, et al. The Four Homeostasis Knights: In Balance upon Post-Translational Modifications. International Journal of Molecular Sciences; 2022; 23: 14480.