Sökning: "empirical valence bond method"

Visar resultat 1 - 5 av 10 avhandlingar innehållade orden empirical valence bond method.

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

    Författare :Masoud Kazemi; Johan Åqvist; Per E. M. Siegbahn; Uppsala universitet; []
    Nyckelord :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;

    Sammanfattning : 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. LÄS MER

  3. 2. Computational modelling of enzyme selectivity

    Författare :Paul Bauer; Shina Caroline Lynn Kamerlin; Mikael Widersten; Kenneth Ruud; Uppsala universitet; []
    Nyckelord :NATURVETENSKAP; NATURAL SCIENCES; enantiomer; epoxide hydrolase; chiral catalysis; empirical valence bond approach; method development; Biokemi; Biochemistry;

    Sammanfattning : Enantioselective reactions are one of the ways to produce pure chiral compounds. Understanding the basis of this selectivity makes it possible to guide enzyme design towards more efficient catalysts. LÄS MER

  4. 3. Ligand binding and enzyme catalysis studied by molecular dynamics simulations

    Författare :Tomas Hansson; Uppsala universitet; []
    Nyckelord :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;

    Sammanfattning : 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. LÄS MER

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

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

    Sammanfattning : 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. LÄS MER

  7. 5. Molecular Simulation of Enzyme Catalysis and Inhibition

    Författare :Sinisa Bjelic; Johan Åqvist; Adrian J. Mulholland; Uppsala universitet; []
    Nyckelord :Theoretical chemistry; enzyme catalysis; enzyme inhibition; computer simulations; molecular dynamics; empirical valence bond method; structure-based inhibitor design; Teoretisk kemi;

    Sammanfattning : The reaction mechanisms for the hemoglobin degrading enzymes in the Plasmodium falciparum malaria parasite, plasmepsin II (Plm II) and histo-aspartic protease (HAP), have been analyzed by molecular simulations. The reaction free energy profiles, calculated by the empirical valence bond (EVB) method in combination with molecular dynamics (MD) and free energy perturbation (FEP) simulations are in good agreement with experimental data. LÄS MER