Matching Items (2)
Description
Conformational changes in biomolecules often take place on longer timescales than are easily accessible with unbiased molecular dynamics simulations, necessitating the use of enhanced sampling techniques, such as adaptive umbrella sampling. In this technique, the conformational free energy is calculated in terms of a designated set of reaction coordinates. At the same time, estimates of this free energy are subtracted from the potential energy in order to remove free energy barriers and cause conformational changes to take place more rapidly. This dissertation presents applications of adaptive umbrella sampling to a variety of biomolecular systems. The first study investigated the effects of glycosylation in GalNAc2-MM1, an analog of glycosylated macrophage activating factor. It was found that glycosylation destabilizes the protein by increasing the solvent exposure of hydrophobic residues. The second study examined the role of bound calcium ions in promoting the isomerization of a cis peptide bond in the collagen-binding domain of Clostridium histolyticum collagenase. This study determined that the bound calcium ions reduced the barrier to the isomerization of this peptide bond as well as stabilizing the cis conformation thermodynamically, and identified some of the reasons for this. The third study represents the application of GAMUS (Gaussian mixture adaptive umbrella sampling) to on the conformational dynamics of the fluorescent dye Cy3 attached to the 5' end of DNA, and made predictions concerning the affinity of Cy3 for different base pairs, which were subsequently verified experimentally. Finally, the adaptive umbrella sampling method is extended to make use of the roll angle between adjacent base pairs as a reaction coordinate in order to examine the bending both of free DNA and of DNA bound to the archaeal protein Sac7d. It is found that when DNA bends significantly, cations from the surrounding solution congregate on the concave side, which increases the flexibility of the DNA by screening the repulsion between phosphate backbones. The flexibility of DNA on short length scales is compared to the worm-like chain model, and the contribution of cooperativity in DNA bending to protein-DNA binding is assessed.
ContributorsSpiriti, Justin Matthew (Author) / van der Vaart, Arjan (Thesis advisor) / Chizmeshya, Andrew (Thesis advisor) / Matyushov, Dmitry (Committee member) / Fromme, Petra (Committee member) / Arizona State University (Publisher)
Created2011
Description
A comprehensive and systematic investigation on the diffusion and phase behaviors of nanoparticles and macromolecules in two component liquid-liquid systems via Molecule Dynamic (MD) simulations is presented in this dissertation.
The interface of biphasic liquid systems has attracted great attention because it offers a simple, flexible, and highly reproducible template for the assembly of a variety of nanoscale objects. However, certain important fundamental issues at the interface have not been fully explored, especially when the size of the object is comparable with the liquid molecules. In the first MD simulation system, the diffusion and self-assembly of nanoparticles with different size, shape and surface composition were studied in an oil/water system. It has been found that a highly symmetrical nanoparticle with uniform surface (e.g. buckyball) can lead to a better-defined solvation shell which makes the “effective radius” of the nanoparticle larger than its own radius, and thus, lead to slower transport (diffusion) of the nanoparticles across the oil-water interface. Poly(N-isopropylacrylamide) (PNIPAM) is a thermoresponsive polymer with a Lower Critical Solution Temperature (LCST) of 32°C in pure water. It is one of the most widely studied stimulus-responsive polymers which can be fabricated into various forms of smart materials. However, current understanding about the diffusive and phase behaviors of PNIPAM in ionic liquids/water system is very limited. Therefore, two biphasic water-ionic liquids (ILs) systems were created to investigate the interfacial behavior of PNIPAM in such unique liquid-liquid interface. It was found the phase preference of PNIPAM below/above its LCST is dependent on the nature of ionic liquids. This potentially allows us to manipulate the interfacial behavior of macromolecules by tuning the properties of ionic liquids and minimizing the need for expensive polymer functionalization. In addition, to seek a more comprehensive understanding of the effects of ionic liquids on the phase behavior of PNIPAM, PNIPAM was studied in two miscible ionic liquids/water systems. The thermodynamic origin causes the reduction of LCST of PNIPAM in imidazolium based ionic liquids/water system was found. Energy analysis, hydrogen boding calculation and detailed structural quantification were presented in this study to support the conclusions.
The interface of biphasic liquid systems has attracted great attention because it offers a simple, flexible, and highly reproducible template for the assembly of a variety of nanoscale objects. However, certain important fundamental issues at the interface have not been fully explored, especially when the size of the object is comparable with the liquid molecules. In the first MD simulation system, the diffusion and self-assembly of nanoparticles with different size, shape and surface composition were studied in an oil/water system. It has been found that a highly symmetrical nanoparticle with uniform surface (e.g. buckyball) can lead to a better-defined solvation shell which makes the “effective radius” of the nanoparticle larger than its own radius, and thus, lead to slower transport (diffusion) of the nanoparticles across the oil-water interface. Poly(N-isopropylacrylamide) (PNIPAM) is a thermoresponsive polymer with a Lower Critical Solution Temperature (LCST) of 32°C in pure water. It is one of the most widely studied stimulus-responsive polymers which can be fabricated into various forms of smart materials. However, current understanding about the diffusive and phase behaviors of PNIPAM in ionic liquids/water system is very limited. Therefore, two biphasic water-ionic liquids (ILs) systems were created to investigate the interfacial behavior of PNIPAM in such unique liquid-liquid interface. It was found the phase preference of PNIPAM below/above its LCST is dependent on the nature of ionic liquids. This potentially allows us to manipulate the interfacial behavior of macromolecules by tuning the properties of ionic liquids and minimizing the need for expensive polymer functionalization. In addition, to seek a more comprehensive understanding of the effects of ionic liquids on the phase behavior of PNIPAM, PNIPAM was studied in two miscible ionic liquids/water systems. The thermodynamic origin causes the reduction of LCST of PNIPAM in imidazolium based ionic liquids/water system was found. Energy analysis, hydrogen boding calculation and detailed structural quantification were presented in this study to support the conclusions.
ContributorsGao, Wei (Author) / Dai, Lenore (Thesis advisor) / Jiao, Yang (Committee member) / Liu, Yongming (Committee member) / Green, Matthew (Committee member) / Emady, Heather (Committee member) / Arizona State University (Publisher)
Created2017