Tracking fluctuation hotspots on the yeast ribosome through the elongation cycle.
Chemical modification was used to quantitatively determine the flexibility of nearly the entire rRNA component of the yeast ribosome through 8 discrete stages of translational elongation, revealing novel observations at the gross and fine-scales. These include (i) the bulk transfer of energy through the intersubunit bridges from the large to the small subunit after peptidyltransfer, (ii) differences in the interaction of the sarcin ricin loop with the two elongation factors and (iii) networked information exchange pathways that may functionally facilitate intra- and intersubunit coordination, including the 5.8S rRNA. These analyses reveal hot spots of fluctuations that set the stage for large-scale conformational changes essential for translocation and enable the first molecular dynamics simulation of an 80S complex. Comprehensive datasets of rRNA base flexibilities provide a unique resource to the structural biology community that can be computationally mined to complement ongoing research toward the goal of understanding the dynamic ribosome.
Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA.
Suna P
SP
Gulay
Department of Computer Science, University of Maryland, College Park, MD 20742, USA.
Sujal
S
Bista
Department of Computer Science, University of Maryland, College Park, MD 20742, USA.
Amitabh
A
Varshney
Chemistry Program, New York University Abu Dhabi, Abu Dhabi, UAE.|The New Mexico Consortium, Los Alamos, NM 87544, USA.
Serdal
S
Kirmizialtin
The New Mexico Consortium, Los Alamos, NM 87544, USA.|Theoretical Biology and Biophysics, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
Karissa Y
KY
Sanbonmatsu
Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA.
Jonathan D
JD
Dinman
D001665:Binding Sites; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D010441:Peptide Chain Elongation, Translational; D010445:Peptide Elongation Factors / Q000737:chemistry / Q000235:genetics; D014176:Protein Biosynthesis / Q000235:genetics; D012335:RNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D012340:RNA, Ribosomal, 5.8S / Q000737:chemistry* / Q000235:genetics; D012270:Ribosomes / Q000737:chemistry / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000737:chemistry / Q000235:genetics
D010445:Peptide Elongation Factors; D012335:RNA, Ribosomal; D012340:RNA, Ribosomal, 5.8S