Protein Folding Simulations: Confinement, External Fields and Sequence Design

The present Thesis looks at the problem of protein folding using Monte Carlo and Langevin simulations, three topics in protein folding have been studied: 1) the effect of confining potential barriers, 2) the effect of a static external field and 3) the design of amino acid sequences which fold in a short time and which have a stable native state (global minimum). Regarding the first topic, we studied the confinement of a small protein of 16 amino acids known as 1NJ0 (PDB code) which has a beta-sheet structure as a native state. The confinement of proteins occurs frequently in the cell environment. Some molecules called Chaperones, present in the cytoplasm, capture the unfolded proteins in their interior and avoid the formation of aggregates and misfolded proteins. This mechanism of confinement mediated by Chaperones is not yet well understood. In the present work we considered two kinds of potential barriers which try to mimic the confinement induced by a Chaperon molecule. The first kind of potential was a purely repulsive barrier whose only effect is to create a cavity where the protein folds up correctly. The second kind of potential was a barrier which includes both attractive and repulsive effects. We performed Wang-Landau simulations to calculate the thermodynamical properties of 1NJ0. From the free energy landscape plot we found that 1NJ0 has two intermediate states in the bulk (without confinement) which are clearly separated from the native and the unfolded states. For the case of the purely repulsive barrier we found that the intermediate states get closer to each other in the free energy landscape plot and eventually they collapse into a single intermediate state. The unfolded state is more compact, compared to that in the bulk, as the size of the barrier decreases. For an attractive barrier modifications of the states (native, unfolded and intermediates) are observed depending on the degree of attraction between the protein and the walls of the barrier. The strength of the attraction is measured by the parameter $\epsilon$. A purely repulsive barrier is obtained for $\epsilon=0$ and a purely attractive barrier for $\epsilon=1$. The states are changed slightly for magnitudes of the attraction up to $\epsilon=0.4$. The disappearance of the intermediate states of 1NJ0 is already observed for $\epsilon =0.6$. A very high attractive barrier ($\epsilon \sim 1.0$) produces a completely denatured state. In the second topic of this Thesis we dealt with the interaction of a protein with an external electric field. We demonstrated by means of computer simulations, specifically by using the Wang-Landau algorithm, that the folded, unfolded, and intermediate states can be modified by means of a field. We have found that an external field can induce several modifications in the thermodynamics of these states: for relatively low magnitudes of the field ($<2.06 \times 10^8$ V/m) no major changes in the states are observed. However, for higher magnitudes than ($6.19 \times 10^8$ V/m) one observes the appearance of a new native state which exhibits a helix-like structure. In contrast, the original native state is a $\beta$-sheet structure. In the new native state all the dipoles in the backbone structure are aligned parallel to the field. The design of amino acid sequences constitutes the third topic of the present work. We have tested the Rate of Convergence criterion proposed by D. Gridnev and M. Garcia ({\it work unpublished}). We applied it to the study of off-lattice models. The Rate of Convergence criterion is used to decide if a certain sequence will fold up correctly within a relatively short time. Before the present work, the common way to decide if a certain sequence was a good/bad folder was by performing the whole dynamics until the sequence got its native state (if it existed), or by studying the curvature of the potential energy surface. There are some difficulties in the last two approaches. In the first approach, performing the complete dynamics for hundreds of sequences is a rather challenging task because of the CPU time needed. In the second approach, calculating the curvature of the potential energy surface is possible only for very smooth surfaces. The Rate of Convergence criterion seems to avoid the previous difficulties. With this criterion one does not need to perform the complete dynamics to find the good and bad sequences. Also, the criterion does not depend on the kind of force field used and therefore it can be used even for very rugged energy surfaces.

The status and barriers to the implementation and continuation of the school gardening projects in Germany, Nigeria and the United States of America

In drawing a conclusion for this study, care must be taken in generalizing findings since the population of students and teachers investigated were limited to certain levels in the different schools and countries. This study recognized some complexity of the factors underlying the status of school gardening instruction and activities in Germany, Nigeria and the U.S. as inadequate time for decision-making in the process of gardening, motivation of teachers and students. This was seen as the major impediments that influenced the status of gardening in the three countries. However, these factors were considered to have affected students’ mode of participation in the school gardening projects. This research finding suggests that the promotion and encouragement of students in gardening activities will promote vegetable production and increasing the numbers of practical farmers. Gardening has the potential to create opportunities for learning in an environment where children are able to experience nature first hand and to use the shared experience for communication (Bowker & Tearle, 2007). Therefore, the need for students to be encouraged to participate in gardening programs as the benefit will not only reduce the rate of obesity currently spreading among youths, but will contribute to the improve knowledge on science subjects. To build a network between community, parents and schools, a parent’s community approach should be used as the curriculum. The community approach will tighten the link between schools; community members, parents, teachers and students. This will help facilitate a better gardening projects implementation. Through a close collaboration, teachers and students will be able to identify issues affecting communities and undertake action learning in collaboration with community organizations to assess community needs and plan the implementation strategies as parents are part of the community. The sense of efficacy is a central factor in motivational and learning processes that govern educational improvement, standard and performance on complex tasks of both teachers and students. Dedication and willingness are the major stimulator and achievement of a project. Through a stimulator and provision of incentives and facilities, schools can achieve the best in project development. Teachers and principals should be aware that students are the lever for achieving the set goals in schools. Failure to understand what students need will result in achieving zero result. Therefore, it is advised that schools focus more on how to lure students to work through proper collaboration with the parents and community members. Principals and teachers should identify areas where students need to be corrected, helping them to correct the problem will enable them be committed in the schools’ programs.