A flexible lattice model to study protein folding

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dc.contributor.advisorHutchinson, John S.en_US
dc.creatorNunes, Nicole Lynneen_US
dc.date.accessioned2009-06-04T00:28:28Zen_US
dc.date.available2009-06-04T00:28:28Zen_US
dc.date.issued1996en_US
dc.description.abstractThe biological activity of protein molecules is central to life. It has been known for decades that this biological activity is dependent on the protein molecule achieving a particular geometric conformation. Simple lattice models have been developed to investigate the protein folding pathway since all-atom molecular dynamics simulations on the time scale of folding are beyond the current capabilities of computers. We present a new Monte Carlo lattice model to study the folding of heteropolymer chains. Previous lattice model studies of two-dimensional chains have been performed on square grids using pre-defined "move sets" of allowed moves. The motion of the polymer chain in these models is thus highly constrained. In order to add greater flexibility, we use a triangular lattice and allow the chain to choose its own moves. Physically unrealistic moves are prevented by including kinetic energy effects in the Metropolis algorithm. By looking at the results, we are able to characterize all of the possible one and two particle moves in the two-dimensional model and sort them according to relative importance. This information will be used to guide simplified molecular dynamics studies. We also find that the initial phase of the folding process is a rapid collapse to a relatively compact state which is entropically driven. The model has been extended to three dimensions. The increased difficulty of working in three-dimensions as well as the preliminary results will be discussed.en_US
dc.format.extent40 p.en_US
dc.format.mimetypeapplication/pdfen_US
dc.identifier.callnoTHESIS CHEM. 1996 NUNESen_US
dc.identifier.citationNunes, Nicole Lynne. "A flexible lattice model to study protein folding." (1996) Diss., Rice University. <a href="https://hdl.handle.net/1911/16929">https://hdl.handle.net/1911/16929</a>.en_US
dc.identifier.urihttps://hdl.handle.net/1911/16929en_US
dc.language.isoengen_US
dc.rightsCopyright is held by the author, unless otherwise indicated. Permission to reuse, publish, or reproduce the work beyond the bounds of fair use or other exemptions to copyright law must be obtained from the copyright holder.en_US
dc.subjectPhysical chemistryen_US
dc.subjectBiochemistryen_US
dc.titleA flexible lattice model to study protein foldingen_US
dc.typeThesisen_US
dc.type.materialTexten_US
thesis.degree.departmentChemistryen_US
thesis.degree.disciplineNatural Sciencesen_US
thesis.degree.grantorRice Universityen_US
thesis.degree.levelDoctoralen_US
thesis.degree.nameDoctor of Philosophyen_US
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