Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 11 of 11 for “"continuum electrostatics"”.
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Structure-function relationship of archaeal rhodopsin proteins analyzed by continuum electrostatics
… thesis, calculations are presented based on a continuum electrostatics approach using a finite-difference discretization of the Poisson-Boltzmann equation. The results can be divided into three parts. One of the interesting features of rhodopsin proteins is the extreme range over which the …
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A Continuum Electrostatic Approach for Calculating The Binding Energetics of Multiple Ligands
… and those, which can be calculated by continuum electrostatics, molecular mechanics and quantum chemistry. Programs (i.e., QMPB and Perl Molecule) were developed to perform calculations based on the generalized ligand binding theory. The class library Perl Molecule was developed to …
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Molecular dynamics studies of membranes and membrane proteins
… simulations, free energy perturbation theory and continuum electrostatics calculations. Three systems were investigated: (1) The proton pump cycle of the integral membrane protein bacteriorhodopsin: The photoisomerization and subsequent thermal reactions of the protein were studied by molecular …
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Conservation of Electrostatically Mediated Function Across Protein Families and Superfamilies
… proven robust enough to probe enzyme function. Continuum electrostatics methods (based on the Poisson-Boltzmann equation) provide a cornputationally efficient method for calculating electrostatic properties of biological molecules. The insights from these methods show that the electrostatically …
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Protein design with hierarchical treatment of solvation and electrostatics
… multiple-site titration and protein design. The continuum electrostatic model is combined with covalent, van der Waals, and non-polar energy terms, and the statistical mechanical basis for this model is reviewed. Multiple-site titration is modeled with four titratable residues of the protein …
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Computer simulation of titration behavior in proteins
… of proteins can be successfully modeled using continuum electrostatic methods provided that a sufficiently detailed and accurate model of the protein system is used. In this work, the effects of conformational changes on calculated pK$\rm\sb{a}$ values in peptide and protein systems are …
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Electrostatic and quantum chemical investigation of the proton pumping mechanism of cytochrome c oxidase
… functional theory is used in combination with continuum electrostatics to calculate the pKa values of these imidazole rings in the aqueous solution as well as in the protein. The pKa values of His334, His333 and H2 O molecule are calculated both in oxidized and reduced state of CuB center. The …
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Monte Carlo Simulation Methods for Studying the Thermodynamics of Ligand Binding & Transfer Processes in Biomolecules
… systems were described by microstates within a continuum electrostatics/molecular mechanics (CE/MM) model of the receptor-ligand system. The CE/MM modeling methodology was improved. The improvements led to more detailed molecular models that enable a more realistic reproduction of system …
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Simulation Studies of Biological Ion Channels
Biological ion channels are responsible for, and regulate the communication system in the body. In this thesis I develop, test and apply theoretical models of ion channels, that can relate their structure to their functional properties. Brownian dynamics simulations are introduced, in which the …
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Simulation Studies of Biological Ion Channels
Biological ion channels are responsible for, and regulate the communication system in the body. In this thesis I develop, test and apply theoretical models of ion channels, that can relate their structure to their functional properties. Brownian dynamics simulations are introduced, in which the …
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Molecular determinants of conductance and charge-selectivity in pentameric ligand-gated ion channels
… such as molecular dynamics, Brownian dynamics, continuum electrostatics, and bioinformatics, which are then compared to experimental data. In the first part, the molecular mechanism of conductance through the cation-selective nicotinic AChR from muscle is studied. In the second part, the …