Commun. Comput. Phys., 7 (2010), pp. 283-300. Transition States in Protein Folding Thomas R. Weikl 1*1 Max Planck Institute of Colloids and Interfaces, Department of Theory and Bio-Systems, 14424 Potsdam, Germany. Received 10 August 2008; Accepted (in revised version) 4 February 2009 Available online 24 August 2009 doi:10.4208/cicp.2009.08.202 Abstract The folding dynamics of small single-domain proteins is a current focus of simulations and experiments. Many of these proteins are 'two-state folders', i.e. proteins that fold rather directly from the denatured state to the native state, without populating metastable intermediate states. A central question is how to characterize the instable, partially folded conformations of two-state proteins, in particular the rate-limiting transition-state conformations between the denatured and the native state. These partially folded conformations are short-lived and cannot be observed directly in experiments. However, experimental data from detailed mutational analyses of the folding dynamics provide indirect access to transition states. The interpretation of these data, in particular the reconstruction of transition-state conformations, requires simulation and modeling. The traditional interpretation of the mutational data aims to reconstruct the degree of structure formation of individual residues in the transition state, while a novel interpretation aims at degrees of structure formation of cooperative substructures such as $\alpha$-helices and $\beta$-hairpins. By splitting up mutation-induced free energies into secondary and tertiary structural components, the novel interpretation resolves some of the inconsistencies of the traditional interpretation. Notice: Undefined variable: ams in /var/www/html/issue/abstract/readabs.php on line 163 PACS: 87.14.E-, 82.20.Db, 87.15.hm Key words: Protein folding, transition-state theory, molecular dynamics, mutational analysis. *Corresponding author. Email: thomas.weikl@mpikg.mpg.de (T. R. Weikl)