Search for dissertations about: "molecular dynamics simulation peptides"

Showing result 1 - 5 of 6 swedish dissertations containing the words molecular dynamics simulation peptides.

2. 1. Fighting microbial infections with force fields: Evaluating conformational ensembles of intrinsically disordered proteins

   Author : Stephanie Jephthah; Beräkningskemi; []
   Keywords : NATURVETENSKAP; NATURAL SCIENCES; molecular dynamics; force field; Monte Carlo; coarse-grained modeling; simulation; intrinsically disordered protein; histatin 5; small-angle x-ray scattering; circular dichroism; atomistic MD simulations; all-atom protein models;

   Abstract : The main goal of this compilation thesis has been to investigate the conformational ensemble of the intrinsically disordered protein (IDP) histatin 5 by using a mixture of experimental and computational techniques including, but not limited to, small-angle X-ray scattering (SAXS), circular dichroism (CD) spectroscopy, atomistic molecular dynamics (MD) simulations, and coarse-grained Monte Carlo (MC) simulations. Histatin 5 is a peptide of particular interest for two reasons. READ MORE

4. 2. Conformational Studies of Biologically Active Peptides

   Author : Björn Walse; Biofysikalisk kemi; []
   Keywords : NATURVETENSKAP; NATURAL SCIENCES; PapD chaperone; P pili; desmopressin; DDAVP; protein-peptide interactions; glycopeptides; peptide design; transferred NOE; molecular dynamics simulations; circular dichroism; peptide conformation; NMR spectroscopy; immunogenic glycopeptides; Physical chemistry; Fysikalisk kemi;

   Abstract : In this work conformational studies have been performed on peptides from four different systems in an attempt to gain knowledge about their biological function. Circular dichroism (CD) spectroscopy and nuclear magnetic resonance (NMR) spectroscopy in combination with distance geometry and restrained molecular dynamics simulations were the methods used. READ MORE

5. 3. Nuclear hormone receptors studied by molecular dynamics computer simulations

   Author : Peter Carlsson; Karolinska Institutet; Karolinska Institutet; []
   Keywords : Nuclear hormone receptor; glucocorticoid; molecular dynamics; simulation; ligand; coactivator; protein; solvation;

   Abstract : Nuclear hormone receptors form a super family of homologous transcription factors. The liganddependent nuclear receptors are important drug targets controlling metabolic and inflammatory disorders, amongst others. READ MORE

6. 4. Computational Studies of Protein-ligand Systems Using Enhanced Sampling Methods

   Author : Rongfeng Zou; Yaoquan Tu; Leif Eriksson; KTH; []
   Keywords : molecular dynamics; enhanced sampling; protein-ligand interactions; umbrella sampling; metadynamics; Teoretisk kemi och biologi; Theoretical Chemistry and Biology;

   Abstract : This thesis focuses on studies of protein-ligand systems using enhanced sampling methods. In chapter I, I give a brief introduction to the time-scale problem and some enhanced sampling methods. In chapter II, the basics of MD simulation are reviewed. READ MORE

7. 5. Structure and spectroscopy of bio- and nano-materials from first-principles simulations

   Author : Weijie Hua; Yi LUO; Mauro Stener; KTH; []
   Keywords : NATURVETENSKAP; NATURAL SCIENCES; NATURVETENSKAP; NATURAL SCIENCES; soft x-ray spectroscopy; bio- and nano-materials; first-principles simulation; host-guest interaction; generalized energy-based fragmentation; Quantum chemistry; Kvantkemi; Spectroscopy; Spektroskopi; SRA - Molecular Bioscience; SRA - Molekylär biovetenskap;

   Abstract : This thesis is devoted to first-principles simulations of bio- and nano-materials,focusing on various soft x-ray spectra, ground-state energies and structures of isolated largemolecules, bulk materials, and small molecules in ambient solutions. K-edge near-edge x-ray absorption fine structure (NEXAFS) spectra, x-ray emission spectra, andresonant inelastic x-ray scattering spectra of DNA duplexes have been studied by means oftheoretical calculations at the density functional theory level. READ MORE