Polyelectrolyte behavior and kinetics of aminoacyl-tRNA on the ribosome.
The torque acting on cognate (three base pairs that are matched) "ternary complex" consisting of elongation factor-Tu, guanosine-5'-triphosphate GTP, and aminoacyl-transfer RNA due to induced wrapping of the 30S subunit of the ribosome and the speed with which the ternary complex samples the space allowed by diffusion is determined. Under appropriate conditions, mode coupling speeds up the barrier crossing rate for cognate relative to near-cognate ternary complexes. We determine the flexibility of the ternary complex relative to transfer RNA (tRNA) by a coarse-grained model. We predict the magnesium binding sites in the ternary complex at low magnesium concentration and unravel the nature of the interaction energy of magnesium with site-specific tRNAPhe bases.
Spasic
A
A
Department of Chemistry, Boston College, Chestnut Hill, MA 02467, USA.
Sitha
S
S
Korchak
M
M
Chu
S
S
Mohanty
U
U
D001665:Binding Sites; D004573:Electrolytes / Q000737:chemistry*; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000378:metabolism; D046911:Macromolecular Substances / Q000737:chemistry / Q000378:metabolism; D008274:Magnesium / Q000737:chemistry; D008958:Models, Molecular; D010444:Peptide Elongation Factor Tu / Q000737:chemistry / Q000378:metabolism; D011108:Polymers / Q000737:chemistry*; D012346:RNA, Transfer, Amino Acyl / Q000737:chemistry* / Q000378:metabolism; D012360:RNA, Transfer, Phe / Q000737:chemistry; D012270:Ribosomes / Q000737:chemistry* / Q000378:metabolism
D004573:Electrolytes; D029968:Escherichia coli Proteins; D046911:Macromolecular Substances; D011108:Polymers; D012346:RNA, Transfer, Amino Acyl; D012360:RNA, Transfer, Phe; D010444:Peptide Elongation Factor Tu; D008274:Magnesium