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We present a simple model of protein folding dynamics that captures key qualitative elements recently seen in all-atom simulations. The goals of this theory are to serve as a simple formalism for gaining deeper insight into the physical properties seen in detailed simulations as well as to serve as a model to easily compare why these simulations suggest a diff…

As the fastest folding protein, the villin headpiece (HP35) serves as an important bridge between simulation and experimental studies of protein folding. Despite the simplicity of this system, experiments continue to reveal a number of surprises, including structure in the unfolded state and complex equilibrium dynamics near the native state. Using 2.5 ms of m…

Two strategies have been recently employed to push molecular simulation to long, biologically relevant time scales: projection-based analysis of results from specialized hardware producing a small number of ultralong trajectories and the statistical interpretation of massive parallel sampling performed with Markov state models (MSMs). Here, we assess the MSM a…

As the resolution of experiments to measure folding kinetics continues to improve, it has become imperative to avoid bias that may come with fitting data to a predetermined mechanistic model. Toward this end, we present a rate spectrum approach to analyze timescales present in kinetic data. Computing rate spectra of noisy time series data via numerical discret…

Markov state models (MSMs) have proven themselves to be effective statistical and quantitative models for understanding protein folding dynamics. As stochastic networks, MSMs allow for descriptions of parallel folding pathways and facilitate quantitative comparison to experiments conducted at the ensemble level. While this complex network structure is advantag…

Markov state models (MSMs) have proven to be useful tools in simulating large and slowly-relaxing biological systems like proteins. MSMs model proteins through dynamics on a discrete-state energy landscape, allowing molecules to effectively sample large regions of phase space. In this work, we use aspects of MSMs to ask: is protein folding mechanistically robu…

Protein folding is a fundamental process in biology, key to understanding many human diseases. Experimentally, proteins often appear to fold via simple two- or three-state mechanisms involving mainly native-state interactions, yet recent network models built from atomistic simulations of small proteins suggest the existence of many possible metastable states a…

Markov state models constructed from molecular dynamics simulations have recently shown success at modeling protein folding kinetics. Here we introduce two methods, flux PCCA+ (FPCCA+) and sliding constraint rate estimation (SCRE), that allow accurate rate models from protein folding simulations. We apply these techniques to fourteen massive simulation dataset…

Motivated by the observed time scales in protein systems said to fold “downhill,” we have studied the finite, linear master equation, with uniform rates forward and backward as a model of the downhill process. By solving for the system eigenvalues, we prove the claim that in situations where there is no free energy barrier a transition between single- and mult…

Quantitatively accurate all-atom molecular dynamics (MD) simulations of protein folding have long been considered a holy grail of computational biology. Due to the large system sizes and long timescales involved, such a pursuit was for many years computationally intractable. Further, sufficiently accurate forcefields needed to be developed in order to realisti…