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Dynamic Function Relationships - Research Paper Example

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Dynamic Function Relationships Name Institution Abstract This study involved describing a novel analysis of the correlation between Cm, Tm, normalized B-factor and F-max for drawing the comparison between the Mechanical Strength of Proteins and their Thermal Stability…
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Download file to see previous pages The study correlated the mechanical strength as measured by F-max with the thermal stability as measured by Tm, Cm, etc. Introduction Atomic force microscopy, the optical tweezers, alongside other nanotechnology tools has made it possible to induce and monitor large conformational changes in biomolecules. These studies are often performed in helping asses the biomolecules structure, their elastic properties, as well as their ability to work as nanomachines in cells. Stretching studies on protein have increasingly become of particular interest and they have been done in systems more than a hundred. All-atom simulation, such as those reported in refs, has helped the interpretation of such experiments possible. However, they have been limited by order 100 ns time scales. They, thus, need the use of large constant pulling speeds, which are quite unrealistic and elucidate the nature of a force clamp (region that is responsible for the force of pulling, which is the largest) Fmax. It is worthwhile noting that virtually all the all-atom, and experimental simulational studies merely address a small fraction of the proteins that are often stored within the Protein Data Bank (PDB). It is, thus, worth considering a large set of proteins in order to determine their largest force of resistance to pulling in any model that allows fast and accurate calculations. In this task, the structure-based model of proteins pioneered by collaborators of Go and applicable is implemented in many projects, seem to be most suitable. This is because the proteins are well defined in respect to the native structure. There are various ways of constructing a structure-based model of proteins. However, their variances differ in the choice of their effective potential, the nature of their local backbone stiffness, course-grained degrees of freedom, and the energy related parameters. The crucial choice concerns making a decision about the interaction between the Count of amino acids as native contacts. Research has shown that organism often try to adapt their proteins in order to function more effectively within their range of environmental temperature. This implies that proteins, in general, have a certain limited temperature range in which the structural range is maintained. Anything that lies outside this specific thermal span causes denaturalization to occur with the corresponding function loss, such as the enzyme activity. Changing the intrinsic thermal stability of proteins can be achieved through alteration of the amino acids or otherwise extrinsically through addition of the suitable stabilizing effectors such as coenzymes, peptides, cations, and membranes. This paper deals with the mechanical strength of proteins and their thermal stability with a focus on making comparison between the two. In order to appropriately make comparison between the mechanical strength of proteins and their thermal stability, there was need to correlation Cm, Tm, and normalized B-factor and F-max. In this regard, a mode of experiment B-factors from the PDB database, the experimental lists of protein resilience, single molecule pulling, and protein motion by ANM were used in this study. Materials and Methods The design method to be applied in this study would be a quantitative research design. In social sciences, quantitative research is used to refer to systematic investigation of a phenomenon through a computation technique. The aim of the quantitative ...Download file to see next pagesRead More
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