Sökning: "solvation free energy"

Visar resultat 1 - 5 av 22 avhandlingar innehållade orden solvation free energy.

  1. 1. Solvation properties of proteins in membranes

    Författare :Anna CV Johansson; Erik Lindahl; Mounir Tarek; Stockholms universitet; []
    Nyckelord :NATURVETENSKAP; NATURAL SCIENCES; membrane protein; lipid bilayer; free energy; solvation; insertion; molecular dynamics simulations; protein mass fraction; Theoretical chemistry; Teoretisk kemi; Biochemistry; biokemi;

    Sammanfattning : Knowledge about the insertion and stabilization of membrane proteins is a key step towards understanding their function and enabling membrane protein design. Transmembrane helices are normally quite hydrophobic to insert efficiently, but there are many exceptions with unfavorable polar or titratable residues. LÄS MER

  3. 2. On the Thermodynamic Solvation of Biomolecules in Solution

    Författare :Stefan Hervö Hansen; Beräkningskemi; []
    Nyckelord :NATURVETENSKAP; NATURAL SCIENCES; Solubility; Solvation; Aggregation; Statistical thermodynamics; Molecular dynamics; Monte Carlo simulations; Free energy calculations; Energy-representation theory of solvation; Proteins; Salt bridges; Caffeine;

    Sammanfattning : The topic solvation thermodynamics is an important aspect of chemistry, dealing with the effects introduced by solvents onto solutes. In particular, biological systems are highly heterogeneous in their choice of solvent typically characterized by either being in a polar or non-polar environment. LÄS MER

  4. 3. Challenges in Computational Biochemistry: Solvation and Ligand Binding

    Författare :Jens Carlsson; Johan Åqvist; Chris Reynolds; Uppsala universitet; []
    Nyckelord :Molecular biology; computer simulations; molecular dynamics; solvation free energy; Generalized-Born; Poisson-Boltzmann; ligand binding; binding free energy; linear interaction energy; binding entropy; hydration entropy; Molekylärbiologi;

    Sammanfattning : Accurate calculations of free energies for molecular association and solvation are important for the understanding of biochemical processes, and are useful in many pharmaceutical applications. In this thesis, molecular dynamics (MD) simulations are used to calculate thermodynamic properties for solvation and ligand binding. LÄS MER

  5. 4. Free energy calculations of G protein-coupled receptor modulation : New methods and applications

    Författare :Willem Jespers; Hugo Gutiérrez-de-Terán; Johan Åqvist; Jonathan Essex; Uppsala universitet; []
    Nyckelord :NATURVETENSKAP; NATURAL SCIENCES; NATURVETENSKAP; NATURAL SCIENCES; G protein-coupled receptor; adenosine receptor; molecular dynamics; free energy perturbation; homology modeling; computer simulations; conformational selectivity; binding free energy.; Biology with specialization in Molecular Biotechnology; Biologi med inriktning mot molekylär bioteknik;

    Sammanfattning : G protein-coupled receptors (GPCRs) are membrane proteins that transduce the signals of extracellular ligands, such as hormones, neurotransmitters and metabolites, through an intracellular response via G proteins. They are abundant in human physiology and approximately 34% of the marketed drugs target a GPCR. LÄS MER

  7. 5. Computational Methods for Calculation of Ligand-Receptor Binding Affinities Involving Protein and Nucleic Acid Complexes

    Författare :Martin Almlöf; Johan Åqvist; Chris Oostenbrink; Uppsala universitet; []
    Nyckelord :Theoretical chemistry; computer simulations; molecular dynamics; linear interaction energy; binding free energy; linear response; protein-protein interactions; structure-based design; point mutations; hot spots; solvation free energy; Teoretisk kemi;

    Sammanfattning : The ability to accurately predict binding free energies from computer simulations is an invaluable resource in understanding biochemical processes and drug action. Several methods based on microscopic molecular dynamics simulations exist, and in this thesis the validation, application, and development of the linear interaction energy (LIE) method is presented. LÄS MER