Sökning: "empirical valence bond"

Visar resultat 6 - 10 av 19 avhandlingar innehållade orden empirical valence bond.

1. 6. 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

3. 7. 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

4. 8. Computational Studies of Enzymatic Enolization Reactions and Inhibitor Binding to a Malarial Protease

   Författare :Isabella Feierberg; Modesto Orozco; Uppsala universitet; []
   Nyckelord :NATURVETENSKAP; NATURAL SCIENCES; Theoretical chemistry; enzyme mechanism; enolate; molecular dynamics; empirical valence bond; glyoxalase I; ketosteroid isomerase; triosephosphate isomerase; malaria; aspartic protease; plasmepsin; linear interaction energy; drug design; Teoretisk kemi; Theoretical chemistry; Teoretisk kemi; Molecular Biotechnology; Molekylär bioteknik;

   Sammanfattning : Enolate formation by proton abstraction from an sp3-hybridized carbon atom situated next to a carbonyl or carboxylate group is an abundant process in nature. Since the corresponding nonenzymatic process in water is slow and unfavorable due to high intrinsic free energy barriers and high substrate pKa s, enzymes catalyzing such reaction steps must overcome both kinetic and thermodynamic obstacles. LÄS MER

5. 9. 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

7. 10. Promiscuity and Selectivity in Phosphoryl Transferases

   Författare :Alexandre Barrozo; Shina Kamerlin; Qiang Cui; Uppsala universitet; []
   Nyckelord :NATURVETENSKAP; NATURAL SCIENCES; phosphate chemistry; linear free energy relationships; phosphatase; catalytic promiscuity; empirical valence bond approach; alkaline phosphatase;

   Sammanfattning : Phosphoryl transfers are essential chemical reactions in key life processes, including energy production, signal transduction and protein synthesis. They are known for having extremely low reaction rates in aqueous solution, reaching the scale of millions of years. LÄS MER