Search for dissertations about: "Empirical valence bond"

Showing result 1 - 5 of 19 swedish dissertations containing the words Empirical valence bond.

2. 1. Calculations of Reaction Mechanisms and Entropic Effects in Enzyme Catalysis

   Author : Masoud Kazemi; Johan Åqvist; Per E. M. Siegbahn; Uppsala universitet; []
   Keywords : NATURVETENSKAP; NATURAL SCIENCES; NATURVETENSKAP; NATURAL SCIENCES; Enzyme catalysis; Entropy; Cytidine deamination; Ribosome; Peptidyl-tRNA hydrolysis; Peptide bond formation; Empirical valence bond method; Density functional theory; Biology with specialization in Structural Biology; Biologi med inriktning mot strukturbiologi; Biokemi; Biochemistry; Biology with specialization in Molecular Biotechnology; Biologi med inriktning mot molekylär bioteknik;

   Abstract : Ground state destabilization is a hypothesis to explain enzyme catalysis. The most popular interpretation of it is the entropic effect, which states that enzymes accelerate biochemical reactions by bringing the reactants to a favorable position and orientation and the entropy cost of this is compensated by enthalpy of binding. READ MORE

4. 2. Computer simulations of ribosome reactions

   Author : Stefan Trobro; Johan Åqvist; Arieh Warshel; Uppsala universitet; []
   Keywords : Molecular biology; ribosomal termination; Empirical valence bond; peptidyl transfer; Molekylärbiologi;

   Abstract : Peptide bond formation and translational termination on the ribosome have been simulated by molecular mechanics, free energy perturbation, empirical valence bond (MD/FEP/EVB) and automated docking methods. Recent X-ray crystallographic data is used here to calculate the entire free energy surface for the system complete with substrates, ribosomal groups, solvent molecules and ions. READ MORE

5. 3. Computational Protein Evolution : Modeling the Selectivity and Promiscuity of Engineered Enzymes

   Author : Klaudia Szeler; Shina C. Lynn Kamerlin; Mikael Widersten; Maria Ramos; Uppsala universitet; []
   Keywords : NATURVETENSKAP; NATURAL SCIENCES; NATURVETENSKAP; NATURAL SCIENCES; NATURVETENSKAP; NATURAL SCIENCES; enzymes; kinetics; catalysis; density functional theory; empirical valence bond; diesters; evolution; promiscuity; Biokemi; Biochemistry;

   Abstract : Enzymes are biological catalysts that significantly increase the rate of all biochemical reactions that take place within cells and are essential to maintain life. Many questions regarding their function remain unknown. READ MORE

6. 4. Computational Modeling of the Mechanisms and Selectivity of Organophosphate Hydrolases

   Author : Miha Purg; Shina C. Lynn Kamerlin; Iñaki Tuñón; Uppsala universitet; []
   Keywords : NATURVETENSKAP; NATURAL SCIENCES; NATURVETENSKAP; NATURAL SCIENCES; Organophosphate Hydrolase; Computational enzymology; MPH; DFPase; PON1; Empirical Valence Bond; EVB;

   Abstract : Computational modeling is becoming an increasingly integral part of (bio)chemistry, providing a powerful complementary view into the dynamics, binding, and reactivity of biochemical systems. In particular, molecular simulations based on multiscale models are now regularly employed in studies of enzymatic reactions, offering invaluable mechanistic insight through the lens of molecular energy landscapes. READ MORE

7. 5. Ligand binding and enzyme catalysis studied by molecular dynamics simulations

   Author : Tomas Hansson; Uppsala universitet; []
   Keywords : NATURVETENSKAP; NATURAL SCIENCES; Molecular biology; molecular dynamics simulation; free energy; linear response; drug design; empirical valence bond; HIV protease; protein tyrosine phosphatase; Molekylärbiologi; Molecular biology; Molekylärbiologi; molekylärbiologi; Molecular Biology;

   Abstract : Molecular dynamics simulations and free energy calculations can be applied to biomolecular systems to predict ligand binding affinities. Combined with hybrid quantum-classical potential energy surfaces, such computations can also be used to probe enzymatic catalysis mechanisms. READ MORE