Sökning: "EVB"

Visar resultat 1 - 5 av 12 avhandlingar innehållade ordet EVB.

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

    Författare :Miha Purg; Shina C. Lynn Kamerlin; Iñaki Tuñón; Uppsala universitet; []
    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

  3. 2. Enzyme Cold Adaptation through Evolution of Protein Flexibility

    Författare :Jaka Sočan; Johan Åqvist; Hugo Gutiérrez-de-Terán; Janez Mavri; Uppsala universitet; []
    Nyckelord :NATURVETENSKAP; NATURAL SCIENCES; NATURVETENSKAP; NATURAL SCIENCES; EVB; Empirical valence bond method; Pancreatic elastase; α-amylase; Enzyme catalysis; Enzyme evolution; Cold adaptation; Temperature dependence of catalytic rates; Psychrophilic enzyme; Molekylär biovetenskap; Molecular Life Sciences;

    Sammanfattning : What lives, evolves. Macromolecular catalysis is a process, central to both evolutionary and metabolic aspect of life, as it provides a systematic bias favouring certain chemical processes. LÄS MER

  4. 3. Extending the Reach of Computational Approaches to Model Enzyme Catalysis

    Författare :Beat Anton Amrein; Shina Caroline Lynn Kamerlin; Adrian Mulholland; Uppsala universitet; []
    Nyckelord :NATURVETENSKAP; NATURAL SCIENCES; NATURVETENSKAP; NATURAL SCIENCES; NATURVETENSKAP; NATURAL SCIENCES; epoxide hydrolase; enantioselectivity; regioselectivity; enantioconvergence; biocatalysis; empirical valence bond; computational directed evolution;

    Sammanfattning : Recent years have seen tremendous developments in methods for computational modeling of (bio-) molecular systems. Ever larger reactive systems are being studied with high accuracy approaches, and high-level QM/MM calculations are being routinely performed. LÄS MER

  5. 4. Computer simulations of ribosome reactions

    Författare :Stefan Trobro; Johan Åqvist; Arieh Warshel; Uppsala universitet; []
    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

  7. 5. 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