Constrained hidden Markov models reveal further Hsp90 protein states

Abstract Time series of conformational dynamics in proteins are usually evaluated with hidden Markov models (HMMs). This approach works well if the number of states and their connectivity is known. However, for the multi-domain protein Hsp90, a standard HMM analysis with optimization of the BIC (Bayesian information criterion) cannot explain long-lived states well. Therefore, here we employ constrained HMMs, which neglect transitions between states by including assumptions. Gradually tuning a model with justified and focused changes allows us to improve its effectiveness and the score of the BIC. This became possible by analyzing time traces with several thousand observable transitions and, therefore, superb statistics. In this scheme, we also monitor the residences in the states reconstructed by the model, aiming to find exponentially distributed dwell times. We show how introducing new states can achieve these statistics but also point out limitations, e.g. for substantial similarity of two states connected to a common neighbor. One of the states displays the lowest free energy and could be the idle open ‘waiting state’, in which Hsp90 waits for the binding of nucleotides, cochaperones, or clients.