Sökning: "Empirical Valence Bond"

Visar resultat 1 - 5 av 15 avhandlingar innehållade orden Empirical Valence Bond.

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

    Detta är en avhandling från Uppsala : Acta Universitatis Upsaliensis

    Författare :Masoud Kazemi; Uppsala universitet.; Uppsala universitet.; [2017]
    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

  2. 2. Computer simulations of ribosome reactions

    Detta är en avhandling från Uppsala : Acta Universitatis Upsaliensis

    Författare :Stefan Trobro; Uppsala universitet.; [2008]
    Nyckelord :Molecular biology; ribosomal termination; Empirical valence bond; peptidyl transfer; Molekylärbiologi;

    Sammanfattning : 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. LÄS MER

  3. 3. Computational Modeling of the Mechanisms and Selectivity of Organophosphate Hydrolases

    Detta är en avhandling från Uppsala : Acta Universitatis Upsaliensis

    Författare :Miha Purg; Uppsala universitet.; [2018]
    Nyckelord :NATURVETENSKAP; NATURAL SCIENCES; NATURVETENSKAP; NATURAL SCIENCES; Organophosphate Hydrolase; Computational enzymology; MPH; DFPase; PON1; Empirical Valence Bond; EVB;

    Sammanfattning : 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. LÄS MER

  4. 4. Computational Modeling of the Structure, Function and Dynamics of Biomolecular Systems

    Detta är en avhandling från Uppsala : Acta Universitatis Upsaliensis

    Författare :Yashraj Kulkarni; Uppsala universitet.; [2020]
    Nyckelord :NATURVETENSKAP; NATURAL SCIENCES; NATURVETENSKAP; NATURAL SCIENCES; Molecular Dynamics; Empirical Valence Bond; Enzyme Catalysis; Amyloid Beta; ; Triosephosphate Isomerase; TIM; Computational Biochemistry; Computational Enzymology; Biokemi; Biochemistry;

    Sammanfattning : Proteins are a structurally diverse and functionally versatile class of biomolecules. They perform a variety of life-sustaining biological processes with utmost efficiency. A profound understanding of protein function requires knowledge of its structure. LÄS MER

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

    Detta är en avhandling från Uppsala : Acta Universitatis Upsaliensis

    Författare :Tomas Hansson; Uppsala universitet.; [1998]
    Nyckelord :NATURVETENSKAP; NATURAL SCIENCES; Molecular biology; molecular dynamics simulation; free energy; linear response; drug design; empirical valence bond; HIV protease; protein tyrosine phosphatase; Molekylärbiologi; NATURAL SCIENCES Biology Cell and molecular biology Molecular biology; NATURVETENSKAP Biologi Cell- och molekylärbiologi 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