Normal mode analysis based on an elastic network model for biomolecules in the Protein Data Bank,which uses dihedral angles as independent variables

We have developed a computer program, named PDBETA, that performs normal mode analysis (NMA) based on an elastic network model that uses dihedral angles as independent variables. Taking advantage of the relatively small number of degrees of freedom required to describe a molecular structure in dihedral angle space and a simple potential-energy function independent of atom types, we aimed to develop a program applicable to a full-atom system of any molecule in the Protein Data Bank (PDB). The algorithm for NMA used in PDBETA is the same as the computer program FEDER/2, developed previously. Therefore, the main challenge in developing PDBETA was to find a method that can automatically convert PDB data into molecular structure information in dihedral angle space. Here, we illustrate the performance of PDBETA with a protein–DNA complex, a protein–tRNA complex, and some non-protein small molecules, and show that the atomic fluctuations calculated by PDBETA reproduce the temperature factor data of these molecules in the PDB. A comparison was also made with elastic-network-model based NMA in a Cartesian-coordinate system.     

Single-molecule mechanical folding and unfolding kinetics of armless mitochondrial tRNAArg from Romanomermis culicivorax

The mechanical stability of tRNAs contributes to their biological activities. The mitochondrial tRNA^Arg from Romanomermis culicivorax is the shortest tRNA ever known. This tRNA lacks D- and T-arms, represents a stem-bulge-stem architecture but still folds into a stable tertiary structure. Although its structure had been reported, studies on its mechanical folding and unfolding kinetic characteristics are lacking. Here, we directly measured the single-molecule mechanical folding and unfolding kinetics of the armless mt tRNA^Arg by using optical tweezers in different solution conditions. We revealed a two-step reversible unfolding pathway: the first and large transition corresponds to the unfolding of acceptor stem and bulge below 11 pN, and the second and small transition corresponds to the unfolding of anticodon arm at 12 pN-14 pN. Moreover, the free energy landscapes of the unfolding pathways were reconstructed. We also demonstrated that amino acid-chelated Mg²⁺(aaCM), which mimics the intracellular solution condition, stabilizes the bulge of mitochondrial tRNA^Arg possibly by reducing the topological constraints or stabilizing the possible local non-canonical base pairings within the bulge region. Our study revealed the solution-dependent mechanical stability of an armless mt tRNA, which may shed light on future mt tRNA studies.     

Synthesis of Stable Aminoacyl‐tRNA Analogues Containing Triazole as a Bioisoster of Esters

Stable analogues : An effective synthetic route involving cycloaddition between alkynes and azidonucleosides to afford a new class of stable aminoacyl‐tRNA analogues such as depicted is presented. Biological evaluation showed that theses new compounds act as potent inhibitors of FemX_Wv aminoacyl transferase, a novel drug target.

     

Protein biosynthesis: the codon-specific activation of amino acids.

At the start of protein biosynthesis the amino acids are chemically activated by esterification with transfer ribonucleic acids bearing the appropriate anticodons. The esterification is catalyzed with an exceptionally high specificity by aminoacyl-tRNA synthetases. Current knowledge of the structural properties of the reactants, the course of the reaction, and the reasons for its specificity are summarized.     

ARGINYL-tRNA SYNTHETASE FROM Escherichia coli AFFINITY LABELING WITH 3''''-OXIDIZED tRNA~(Arg)

The covalent modification of E. coli arginyl-tRNA synthetase by the 2',3'-dialdehydederivative of tRNA~(Arg) (tRNA_(ox)~(Arg)) resulted in the complete inactivation of the ATP-PPi ex-change and aminoacylation activities of the enzyme. Sodium dodecyl sulfate polyacrylamide gelelectrophoresis of the ArgRS-tRNA_(ox)~(Arg) covalent complexes indicated that two bands simulta-neously appeared on the gel parallel with inactivation corresponding to different higher mo-lecular weights. This result was different from that of the other aminoacyl-tRNA synthetaselabeling systems as previously reported. Upon the ribonuclease treatment of the modifiedArgRS, less than 15% of both the initial ATP-PPi exchange and aminocylation activities wererecovered. During the whole process of labeling and RNase treatment, the two activities ofthe enzyme were closely associated.