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- W840148207 abstract "Proteins carry out the instructions encoded in genes and are crucial for many important tasksin the living organism. Often the specific three dimensional structure, or fold, of a proteinenables it to carry out a given task. It is an open question whether protein folds have arisenindependently or whether mutations to existing protein sequences have caused switches tonew folds.In the main part of this thesis, consisting of papers I-III, we have investigated protein foldswitching in response to point mutations using computer simuations of coarse-grained mod-els. The basic idea behind coarse-grained models is that by simplifying the description ofproteins, the structure of a large number of model sequences can be determined with reducedcomputational effort. In paper I we exhaustively enumerate protein sequence-structure spacein a simple hydrophobic/polar lattice model, exceeding previous enumerations. This enablesus in particular to analyze mutational pathways and their stability. In paper II we investigatehow protein function changes along a mutational pathway with a sharp switch in fold, usingthe continuous Cβ model. We find that the switch in fold and preferred binding partner donot coincide and that the change in function is more gradual than the switch in fold. In paperIII we hypothesize that fold switches between similar protein folds involve bistable sequences,while fold switches between dissimilar folds occur within a single mutation. In particular, weshow that while the fold switches are driven by changes in energy, configurational entropycan play a significant role in determining when a switch occurs. In paper IV, we analyzethe hybrid Monte Carlo method for biomolecular simulations, which is based on numericalintegration of Newton’s equations of motion. We optimize this method for three systems andfind that a nonuniform integration step can reduce the integration error." @default.
- W840148207 created "2016-06-24" @default.
- W840148207 creator A5017147820 @default.
- W840148207 date "2014-01-01" @default.
- W840148207 modified "2023-10-18" @default.
- W840148207 title "PROTEIN FOLD SWITCHING IN COARSE-GRAINED MODELS" @default.
- W840148207 hasPublicationYear "2014" @default.
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