Proteins on the edge [Elektronische Ressource] : transitions of structure ensembles in protein unfolding and protein-protein binding / presented by Raik Grünberg

Dissertationsubmitted to theCombined Faculties for Natural Sciences and Mathematicsof the Ruperto Carola University ofHeidelberg, Germany,for the degree ofDoctor of Natural Sciencespresented byDiplom Biochemiker Raik Gr nbergborn in Riesaoral examination:Proteins on the edgeTransitions of structure ensembles in proteinunfolding and protein-protein bindingReferees: Prof. Dr. Jeremy C. SmithDr. Michael NilgesContentsZusammenfassung viiSummary ixIntroduction xi1 Structures and ensembles 11.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11.2 Experimental methods for the study of protein dynamics . . . . . 21.2.1 Structure determination . . . . . . . . . . . . . . . . . . . 21.2.2 Dynamic properties . . . . . . . . . . . . . . . . . . . . . 51.2.3 Single molecule experiments . . . . . . . . . . . . . . . . 71.3 Theoretical methods for the study of protein dynamics . . . . . . 91.3.1 Molecular mechanics models . . . . . . . . . . . . . . . . 91.3.2 dynamics simulations . . . . . . . . . . . . . . 111.3.3 Different simulation regimes . . . . . . . . . . . . . . . . 121.3.4 Covariance analysis of simulations . . . . . . . . . . . . . 141.3.5 Entropy estimates . . . . . . . . . . . . . . . . . . . . . . 151.4 Function and dynamics – views in transition . . . . . . . . . . . . 171.4.1 Energy landscape of protein structure . . . . . . . . . . . 171.4.2 Directed unfolding of proteins . . . . . . . . . . . . . . . 191.4.