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Visar resultat 1 - 5 av 19 avhandlingar som matchar ovanstående sökkriterier.

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. 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

4. 3. 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

5. 4. 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

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

   Författare :Yashraj Kulkarni; Shina Kamerlin; Markus Meuwly; Uppsala universitet; []
   Nyckelord :NATURVETENSKAP; NATURAL SCIENCES; NATURVETENSKAP; NATURAL SCIENCES; Molecular Dynamics; Empirical Valence Bond; Enzyme Catalysis; Amyloid Beta; Aβ; 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