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• W1715505871 abstract "The K+ channel Kcv from Paramecium bursaria chlorella virus is the smallest known functional K+ channel. As a minimal working model, this K+ channel protein can be considered close to being prototypical in order to understand basic channel design principles and to gain insight into fundamental transport mechanisms. The objective of this work was the computational study of the impact of various mutations of the Kcv N-Terminus on the Kcv function. By the mean of molecular dynamics simulations of K+ channel models in explicit membrane and explicit solvent, the structure, dynamics, and thermodynamics of alternate model systems was examined on the atomic level. In addition to the wildtype, a hyperactive point mutant (KcvP13A) and two inactive deletion mutants (KcvDN8 and KcvDN14) were examined. The protonation state of a key amino acid (Lys29) was also exhaustingly studied. As a working hypothesis it was assumed that analog topology results in analog functionality. Hence, Kcv homology models were generated as well as KirBac1.1 X-ray structure models adapted in analogy to Kcv. A new method was developed in order to extract reasonable and symmetric expectation structures from very long trajectories. These structures can be compared to structures determined by structural biological methods and can be used as an input for proceeding with advanced methods, like e.g. the Poisson-Boltzmann theory or the 3D-RISM integral equation theory. Latter method was used in order to determin the ionic distribution around the protein. Most important results from this thesis are: 1. A workflow was developed that allows the creation of plausible K+ channel homology models. The quality of such a model is good enough to exhibit a full ion transition cycle during simulation. 2. The interaction of positively charged amino acids in the N-terminal helix with the C-terminus results in mutant dependent saltbridge patterns. Weakening of this interaction correlates with dysfuntion. 3. The N-terminus can act as a steric barrier for the transition of K+ ions and, thus, may contribute to the gating mechanism. 4. The protonation state of Lys29 is crutial for the transition of K+ ions and, thus, may also contribute to the gating mechanism. 5. Funtional analogy between distantly related K+ channels is apparent. 6. The reason for the hyperactivity of the point mutant P13A was not determined satisfactorily. Further investigations are necessary in order to generate more plausible models." @default.
• W1715505871 created "2016-06-24" @default.
• W1715505871 creator A5057220079 @default.
• W1715505871 date "2007-08-01" @default.
• W1715505871 modified "2023-09-28" @default.
• W1715505871 title "Computational study of the kcv potassium channel" @default.
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