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tRNA Molecules (trna + molecule)
Selected AbstractsA generalized higher order kernel energy approximation methodJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 16 2010Stewart N. Weiss Abstract We present a general mathematical model that can be used to improve almost all fragment-based methods for ab initio calculation of total molecular energy. Fragment-based methods of computing total molecular energy mathematically decompose a molecule into smaller fragments, quantum-mechanically compute the energies of single and multiple fragments, and then combine the computed fragment energies in some particular way to compute the total molecular energy. Because the kernel energy method (KEM) is a fragment-based method that has been used with much success on many biological molecules, our model is presented in the context of the KEM in particular. In this generalized model, the total energy is not based on sums of all possible double-, triple-, and quadruple-kernel interactions, but on the interactions of precisely those combinations of kernels that are connected in the mathematical graph that represents the fragmented molecule. This makes it possible to estimate total molecular energy with high accuracy and no superfluous computation and greatly extends the utility of the KEM and other fragment-based methods. We demonstrate the practicality and effectiveness of our model by presenting how it has been used on the yeast initiator tRNA molecule, ytRN (1YFG in the Protein Data Bank), with kernel computations using the Hartree-Fock equations with a limited basis of Gaussian STO-3G type. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] The long-range electrostatic interactions control tRNA,aminoacyl-tRNA synthetase complex formationPROTEIN SCIENCE, Issue 6 2003Dmitry Tworowski 3D, three-dimensional; PDB, Protein Data Bank of experimentally determined 3D structures of proteins; aaRS, aminoacyl-tRNA synthetase Abstract In most cases aminoacyl-tRNA synthetases (aaRSs) are negatively charged, as are the tRNA substrates. It is apparent that there are driving forces that provide a long-range attraction between like charge aaRS and tRNA, and ensure formation of "close encounters." Based on numerical solutions to the nonlinear Poisson-Boltzmann equation, we evaluated the electrostatic potential generated by different aaRSs. The 3D-isopotential surfaces calculated for different aaRSs at 0.01 kT/e contour level reveal the presence of large positive patches,one patch for each tRNA molecule. This is true for classes I and II monomers, dimers, and heterotetramers. The potential maps keep their characteristic features over a wide range of contour levels. The results suggest that nonspecific electrostatic interactions are the driving forces of primary stickiness of aaRSs,tRNA complexes. The long-range attraction in aaRS,tRNA systems is explained by capture of negatively charged tRNA into "blue space area" of the positive potential generated by aaRSs. Localization of tRNA in this area is a prerequisite for overcoming the barrier of Brownian motion. [source] Escherichia coli tRNase Z can shut down growth probably by removing amino acids from aminoacyl-tRNAsGENES TO CELLS, Issue 11 2008Hiroaki Takaku In most organisms, tRNase Z is considered to be essential for 3, processing of tRNA molecules. The Escherichia coli tRNase Z gene, however, appears to be dispensable under normal growth conditions, and its existence remained an enigma. Here we intensively examined various (pre-)tRNAs for good substrates of E. coli tRNase Z in vitro, and found that the enzyme can remove the 3, terminal CCA residues from mature tRNAs regardless of their nucleotide modifications. Furthermore, we discovered that E. coli tRNase Z, when sufficiently expressed in the cell, can shut down growth probably by removing amino acids from aminoacyl-tRNAs. We confirmed in vitro that E. coli tRNase Z exceptionally possesses the activity that cleaves off the 3, terminal residues charging an amino acid from an aminoacyl-tRNA molecule. The current data suggest that tRNase Z might help modulate a cell growth rate by repressing translation under some stressful conditions. [source] Construction and performance of heterologous polyketide-producing K-12- and B-derived Escherichia coliLETTERS IN APPLIED MICROBIOLOGY, Issue 2 2010J. Wu Abstract Aims:,Escherichia coli has emerged as a viable heterologous host for the production of complex, polyketide natural compounds. In this study, polyketide biosynthesis was compared between different E. coli strains for the purpose of better understanding and improving heterologous production. Methods and Results:, Both B and K-12 E. coli strains were genetically modified to support heterologous polyketide biosynthesis [specifically, 6-deoxyerythronolide B (6dEB)]. Polyketide production was analysed using a helper plasmid designed to overcome rare codon usage within E. coli. Each strain was analysed for recombinant protein production, precursor consumption, by-product production, and 6dEB biosynthesis. Of the strains tested for biosynthesis, 6dEB production was greatest for E. coli B strains. When comparing biosynthetic improvements as a function of mRNA stability vs codon bias, increased 6dEB titres were observed when additional rare codon tRNA molecules were provided. Conclusions:,Escherichia coli B strains and the use of tRNA supplementation led to improved 6dEB polyketide titres. Significance and Impact of the Study:, Given the medicinal potential and growing field of polyketide heterologous biosynthesis, the current study provides insight into host-specific genetic backgrounds and gene expression parameters aiding polyketide production through E. coli. [source] Ribosomal crystallography: Peptide bond formation and its inhibitionBIOPOLYMERS, Issue 1 2003Anat Bashan Abstract Ribosomes, the universal cellular organelles catalyzing the translation of genetic code into proteins, are protein/RNA assemblies, of a molecular weight 2.5 mega Daltons or higher. They are built of two subunits that associate for performing protein biosynthesis. The large subunit creates the peptide bond and provides the path for emerging proteins. The small has key roles in initiating the process and controlling its fidelity. Crystallographic studies on complexes of the small and the large eubacterial ribosomal subunits with substrate analogs, antibiotics, and inhibitors confirmed that the ribosomal RNA governs most of its activities, and indicated that the main catalytic contribution of the ribosome is the precise positioning and alignment of its substrates, the tRNA molecules. A symmetry-related region of a significant size, containing about two hundred nucleotides, was revealed in all known structures of the large ribosomal subunit, despite the asymmetric nature of the ribosome. The symmetry rotation axis, identified in the middle of the peptide-bond formation site, coincides with the bond connecting the tRNA double-helical features with its single-stranded 3, end, which is the moiety carrying the amino acids. This thus implies sovereign movements of tRNA features and suggests that tRNA translocation involves a rotatory motion within the ribosomal active site. This motion is guided and anchored by ribosomal nucleotides belonging to the active site walls, and results in geometry suitable for peptide-bond formation with no significant rearrangements. The sole geometrical requirement for this proposed mechanism is that the initial P-site tRNA adopts the flipped orientation. The rotatory motion is the major component of unified machinery for peptide-bond formation, translocation, and nascent protein progression, since its spiral nature ensures the entrance of the nascent peptide into the ribosomal exit tunnel. This tunnel, assumed to be a passive path for the growing chains, was found to be involved dynamically in gating and discrimination. © 2003 Wiley Periodicals, Inc. Biopolymers, 2003 [source] The structure of Rph, an exoribonuclease from Bacillus anthracis, at 1.7,Å resolutionACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 1 2009Andrea E. Rawlings Maturation of tRNA precursors into functional tRNA molecules requires trimming of the primary transcript at both the 5, and 3, ends. Cleavage of nucleotides from the 3, stem of tRNA precursors, releasing nucleotide diphosphates, is accomplished in Bacillus by a phosphate-dependent exoribonuclease, Rph. The crystal structure of this enzyme from B. anthracis has been solved by molecular replacement to a resolution of 1.7,Å and refined to an R factor of 19.3%. There is one molecule in the asymmetric unit; the crystal packing reveals the assembly of the protein into a hexamer arranged as a trimer of dimers. The structure shows two sulfate ions bound in the active-site pocket, probably mimicking the phosphate substrate and the phosphate of the 3,-terminal nucleotide of the tRNA precursor. Three other bound sulfate ions point to likely RNA-binding sites. [source] | |||||||||||||