Dynamical analysis of tRNAGln–GlnRS complex using normal mode calculation

Conformational symmetry and vibrational dynamics of polymers

Polymers are an important class of materials, and their conformation dictates their dynamical, thermodynamical, and hydrodynamical behavior. Several spectroscopic and other techniques have been employed to characterize their conformation. However, little use has been made of group-theoretical techniques except in the classification of symmetry species. In the present review, an attempt has been made to correlate normal modes and their dispersion profiles with the conformation of the polymeric systems. This has been attempted in the case of 2-, 3-, 4-fold and α-helical polymers.

Mechanism of the difference in the binding affinity of E. coli tRNAGln to glutaminyl-tRNA synthetase caused by noninterface nucleotides in variable loop

Aminoacyl-tRNA synthetases (ARSs) distinguish their cognate tRNAs from many other kinds of tRNAs, despite the very similar tertiary structures of tRNAs. Many researchers have supported the view that this recognition is achieved by intermolecular interactions between tRNA and ARS. However, one of the aptamers of Escherichia coli glutamine specific tRNA, var-AGGU, has a higher affinity to ARS than the wild-type, although the sequence difference only lies in the variable loop located on the opposite side of the binding interface with ARS. To understand the reason for the difference in affinity, we did molecular dynamics simulations on tRNAs and their complexes with ARS. We calculated the enthalpic and entropic contributions to the binding free energy with the molecular mechanics-Poisson-Boltzmann/surface area method and found that the entropic difference plays an important role in the difference in binding free energies. During the molecular dynamics simulations, dynamic rearrangements of hydrogen bonds occurred in the tertiary core region of the wild-type tRNA, whereas they were not observed in the free var-AGGU simulation. Since the internal mobility was suppressed upon complex formation with ARS, the entropy loss in the wild-type was larger than that of the aptamer. We therefore concluded that the sequence difference in the variable loop caused the difference in the internal mobility of the tertiary core region tRNAs and led to the difference in the affinity to ARS through the entropy term.

tRNA-isoleucine-tryptophan composite gene

Transfer-RNA genes in archaea often have introns intervening between exon sequences. The structural motif at the boundary between exon and intron is the bulge-helix-bulge. Computational investigations of these boundary structures in Haloarcula marismortui lead us to propose that tRNA-isoleucine and tRNA-tryptophan genes are co-located. Precise in silico identification of the splice-sites on the bulges at the exon-intron boundaries lead us to infer that a single intron-containing composite tRNA-gene can give rise to more than one gene product.