Changes in the level of poly(Phe) synthesis in Escherichia coli ribosomes containing mutants of L4 ribosomal protein from Thermus thermophilus can be explained by structural changes in the peptidyltransferase center: a molecular dynamics simulation analysis.
Data from polyphenylalanine [poly(Phe)] synthesis determination in the presence and in the absence of erythromycin have been used in conjunction with Molecular Dynamics Simulation analysis, in order to localize the functional sites affected by mutations of Thermus thermophilus ribosomal protein L4 incorporated in Escherichia coli ribosomes. We observed that alterations in ribosome capability to synthesize poly(Phe) in the absence of erythromycin were mainly correlated to shifts of A2062 and C2612 of 23S rRNA, while in the presence of erythromycin they were correlated to shifts of A2060 and U2584 of 23S rRNA. Our results suggest a means of understanding the role of the extended loop of L4 ribosomal protein in ribosomal peptidyltransferase center.
Papadopoulos
G
G
Department of Biochemistry and Biotechnology, University of Thessaly, Ploutonos 26, 41221, Larissa, Greece. papg@chem.auth.gr
Grudinin
S
S
Kalpaxis
D L
DL
Choli-Papadopoulou
T
T
D000595:Amino Acid Sequence; D000900:Anti-Bacterial Agents / Q000494:pharmacology; D004917:Erythromycin / Q000494:pharmacology; D004926:Escherichia coli / Q000187:drug effects / Q000235:genetics / Q000378:metabolism*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009154:Mutation; D009690:Nucleic Acid Conformation; D010455:Peptides / Q000378:metabolism*; D010458:Peptidyl Transferases / Q000737:chemistry / Q000378:metabolism*; D011487:Protein Conformation; D012329:RNA, Bacterial / Q000235:genetics; D012338:RNA, Ribosomal, 23S / Q000235:genetics; D012269:Ribosomal Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D012270:Ribosomes / Q000235:genetics / Q000378:metabolism*; D016963:Thermus thermophilus / Q000378:metabolism*
D000900:Anti-Bacterial Agents; D010455:Peptides; D012329:RNA, Bacterial; D012338:RNA, Ribosomal, 23S; D012269:Ribosomal Proteins; C056368:ribosomal protein L4; C012001:polyphenylalanine; D004917:Erythromycin; D010458:Peptidyl Transferases