Sökning: "codon recognition"

Visar resultat 1 - 5 av 10 avhandlingar innehållade orden codon recognition.

1. 1. Computational Analysis of Molecular Recognition Involving the Ribosome and a Voltage Gated K+ Channel

   Författare :Martin Andér; Johan Åqvist; Lennart Nilsson; Uppsala universitet; []
   Nyckelord :NATURVETENSKAP; NATURAL SCIENCES; NATURVETENSKAP; NATURAL SCIENCES; computer simulations; molecular dynamics; ligand binding; binding free energy; linear interaction energy; codon recognition; translation termination; release factor; voltage gated potassium ion channel; Kv1.5; Structural biology; Strukturbiologi; Biochemistry; Biokemi; Biokemi; Biochemistry;

   Sammanfattning : Over the last few decades, computer simulation techniques have been established as an essential tool for understanding biochemical processes. This thesis deals mainly with the application of free energy calculations to ribosomal complexes and a cardiac ion channel. LÄS MER

3. 2. Evolutionary Mechanisms Shaping Bacterial Translation Termination

   Författare :Shreya Pundir; Suparna Sanyal; Martin Ott; Uppsala universitet; []
   Nyckelord :NATURVETENSKAP; NATURAL SCIENCES; NATURVETENSKAP; NATURAL SCIENCES; Ribosome; Protein; Release Factor; Translation; Termination; Stop codon; Evolution; Mutation; Kinetics; Cryo-EM; Molekylär biovetenskap; Molecular Life Sciences;

   Sammanfattning : Translation termination in bacteria involves precise reading of stop codons (UAA, UAG, UGA) and coordinated peptidyl-tRNA hydrolysis by the class-I release factors (RFs) on the ribosome (70S). This thesis investigates the evolutionary and post-translational modification mechanisms of these RFs and the concurrent effect on bacterial translation termination. LÄS MER

4. 3. The Mechanism of translation termination in Escherichia coli

   Författare :David V. Freistroffer; Uppsala universitet; []
   Nyckelord :NATURVETENSKAP; NATURAL SCIENCES; Developmental biology; Utvecklingsbiologi; Developmental biology; Utvecklingsbiologi; molekylärbiologi; Molecular Biology;

   Sammanfattning : Protein synthesis in E. coli is terminated by the release factors (RFs) and the ribosome is prepared for another round of protein synthesis by ribosome recycling factor (RRF), elongation factor G (EF-G) and initiation factor (IF3). LÄS MER

5. 4. Choice of tRNA on Translating Ribosomes

   Författare :Elli Bouakaz; Måns Ehrenberg; Christian Spahn; Uppsala universitet; []
   Nyckelord :NATURVETENSKAP; NATURAL SCIENCES; Molecular biology; Ribosome; Translation; Accuracy; Proofreading; tRNA; Molekylärbiologi; Molecular biology; Molekylärbiologi;

   Sammanfattning : This thesis addresses different aspects of the question about accuracy of protein synthesis: i) the mechanism of tRNA selection during translation ii) study of ribosomal mutations that affect accuracy and iii) the choice of aminoacyl-tRNA isoacceptors on synonymous codons.By measuring the codon reading efficiencies of cognate and near-cognate ternary complexes we demonstrate that in optimal physiological conditions accuracy of substrate selection is much higher than previously reported; that during translation the ribosomal A site is not blocked by unspecific binding of the non-cognate tRNAs which would inhibit the speed of protein synthesis. LÄS MER

7. 5. Computational Methods for Calculation of Ligand-Receptor Binding Affinities Involving Protein and Nucleic Acid Complexes

   Författare :Martin Almlöf; Johan Åqvist; Chris Oostenbrink; Uppsala universitet; []
   Nyckelord :Theoretical chemistry; computer simulations; molecular dynamics; linear interaction energy; binding free energy; linear response; protein-protein interactions; structure-based design; point mutations; hot spots; solvation free energy; Teoretisk kemi;

   Sammanfattning : The ability to accurately predict binding free energies from computer simulations is an invaluable resource in understanding biochemical processes and drug action. Several methods based on microscopic molecular dynamics simulations exist, and in this thesis the validation, application, and development of the linear interaction energy (LIE) method is presented. LÄS MER