The dynamics of a protein plays an important role in protein functionality. Here, we examine the differences in the dynamics of a minimally restructuring protein, EcoRI, when it is bound to its cognate DNA and to a noncognate sequence which differs by just a single basepair. Molecular dynamics simulations of the complexes and essential dynamics analyses reveal that the overall dynamics of the p...

During translation, usually only one in approximately 400 misincorporations affects the function of a nascent protein, because only chemically similar near-cognate amino acids are misincorporated in place of the cognate one. The deleterious misincorporation of a chemically dissimilar noncognate amino acid during the selection process is precluded by the presence of a tRNA at the ribosomal E-sit...

We suggest that the interaction between a codon and its cognate tRNA induces conformational changes in the tRNA. We further suggest that sites on the ribosome preferentially bind tRNA in those conformations which require proper matching of codon and anticodon. According to this model, the codon functions as an allosteric effector which influences the conformation at various sites in the tRNA. T...

Introduction Aminoacyl-tRNA synthetases (aaRSs) play a central role in the assembly of amino acids into polypeptide chains. By selection of the correct amino acid for acylation of a specific tRNA, they provide the key for translation of the genetic code. The 20 aaRSs are divided into two classes of 10 enzymes each. TyrosyltRNA synthetase (TyrRS) is a class I enzyme, but is unusual in that it is...