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European Biophysics Journal

, Volume 35, Issue 8, pp 675–683 | Cite as

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

  • G. Papadopoulos
  • S. Grudinin
  • D. L. Kalpaxis
  • T. Choli-Papadopoulou
Article
  • 75 Downloads

Abstract

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.

Keywords

Molecular dynamics Ribosomal function Erythromycin 

Abbreviations

Poly(Phe)

Polyphenylalanine

PTase

Peptidyltransferase

rRNA

Ribosomal RNA

TthL4

Ribosomal protein L4 from Thermus thermophilus

EcL22

Ribosomal protein L22 from Escherichia coli

MDS

Molecular dynamics simulation

wtTthL4

Wild type L4 from Thermus thermophilus

TthL4-Glu55

TthL4 with Gly55 replaced by Glu

TthL4-Ser55

TthL4 with Gly55 replaced by Ser

TthL4-Asp56

TthL4 with Glu56 replaced by Asp

TthL4-Gln56

TthL4 with Glu56 replaced by Gln

TthL4- Glu55Gly56

TthL4 with Gly55Glu56 inverted

RMSD

Root mean square deviation

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Copyright information

© EBSA 2006

Authors and Affiliations

  • G. Papadopoulos
    • 1
  • S. Grudinin
    • 2
  • D. L. Kalpaxis
    • 3
  • T. Choli-Papadopoulou
    • 4
  1. 1.Department of Biochemistry and BiotechnologyUniversity of ThessalyLarissaGreece
  2. 2.Institute for Structural Biology (IBI-2)Forschungszentrum JülichJülichGermany
  3. 3.Laboratory of Biochemistry, School of MedicineUniversity of PatrasPatrasGreece
  4. 4.Laboratory of Biochemistry, School of ChemistryAristotle University of ThessalonikiThessalonikiGreece

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