Search for dissertations about: "protein-DNA interactions"

Showing result 1 - 5 of 19 swedish dissertations containing the words protein-DNA interactions.

2. 1. Modelling the Protein-DNA Interface

   Author : Malin Lüking; Shina C. Lynn Kamerlin; Ehmke Pohl; Uppsala universitet; []
   Keywords : Protein-DNA interactions; Molecular Dynamics; Coarse-grained simulations; gene regulation; Biokemi; Biochemistry;

   Abstract : Protein-DNA interactions are crucial to life. Several millions of DNA base pair steps are organ- ised, read and protected by proteins in every cell. Protein-DNA interactions must be specific, controllable and reasonably fast. Understanding how these features coexist is one of the great challenges for biochemists and molecular biologists. READ MORE

4. 2. Thermodynamics of protein-DNA interactions

   Author : Thomas Lundbäck; Karolinska Institutet; Karolinska Institutet; []
   Keywords : DNA-protein interactions; molecular recognition; thermodynamics; specificity.dehydration; salt dependence.;

   Abstract : This thesis treats the molecular recognition between DNA-binding proteins and DNA and the way these interactions are affected by the surrounding water solution and dissolved solutes. The work involves studies on the thermodynamics of sequence specific DNA-binding of the human glucocorticoid receptor DNA-binding domain and the nonsequence specific DNA- binding of Sso7d from the archaeon Sulfolobus solfataricus. READ MORE

5. 3. Reaction-Diffusion kinetics of Protein DNA Interactions

   Author : Anel Mahmutovic; Johan Elf; David van der Spoel; Pieter Rein ten Wolde; Uppsala universitet; []
   Keywords : NATURVETENSKAP; NATURAL SCIENCES; NATURVETENSKAP; NATURAL SCIENCES; umbrella sampling; molecular dynamics; RDME; PDE; sliding; intersegment transfer; hopping; sterics; intersegment transfer; Biology with specialization in Molecular Biotechnology; Biologi med inriktning mot molekylär bioteknik;

   Abstract : Transcription factors need to rapidly find one specific binding site among millions of nonspecific sites on the chromosomal DNA. In this thesis I use various aspects of reaction-diffusion theory to investigate the interaction between proteins and DNA and to explain the searching, finding and binding to specific operator sites. READ MORE

6. 4. Studies on Baltic Sea mysids

   Author : Martin Ogonowski; Sture Hansson; Jörgen Berge; Stockholms universitet; []
   Keywords : NATURVETENSKAP; NATURAL SCIENCES; Mysids; hydroacoustics; Baltic Sea; abundance; stable isotopes; specific dynamic action SDA ; diel vertical migration; partial migration; trophic interactions; physiology; benthic-pelagic coupling; protein:DNA; C:N ratio; genetic structure; Marine Ecology; marin ekologi;

   Abstract : Mysid shrimps (Mysidacea, Crustacea) are efficient zooplanktivores in both marine and freshwater systems as well as lipid rich prey for many species of fish.  Although some efforts have been made to study the role of mysids in the Baltic Sea, very few studies have been carried out in recent time and there are still knowledge gaps regarding various aspects of mysid ecology. READ MORE

7. 5. Towards simulating fully charged protein-DNA systems in water : Zif268-DNA as a test case

   Author : Git Roxström; Uppsala universitet; []
   Keywords : NATURVETENSKAP; NATURAL SCIENCES; Physics; Molecular Dynamics simulation; Zif268; zinc fingers; GROMOS; linkers; recognition sites; Fysik; Physics; Fysik; Physical Chemistry; fysikalisk kemi;

   Abstract : In this thesis, we develop a computing strategy to simulate fully charged protein-DNA systems with a general force field (GROMOS87). The ions neutralizing the phosphates (P-ions) are submitted to global symmetry constraints. A model exhibiting ionic-atmosphere effects on mobile P-ions was implemented via very weak restraint forces. READ MORE