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The extent to which glass-like kinetics govern dynamics in protein folding has been heavily debated. Here, we address the subject with an application of space-time perturbation theory to the dynamics of protein folding Markov state models. Borrowing techniques from the s-ensemble method, we argue that distinct active and inactive phases exist for protein foldi…

Markov State Models (MSMs) provide an automated framework to investigate the dynamical properties of high-dimensional molecular simulations. These models can provide a human-comprehensible picture of the underlying process, and have been successfully used to study protein folding, protein aggregation, protein ligand binding, and other biophysical systems. The …

The protein folding problem has long represented a “holy grail” in statistical physics due to its physical complexity and its relevance to many human diseases. While past theoretical work has yielded apt descriptions of protein folding landscapes, recent large-scale simulations have provided insights into protein folding that were impractical to obtain from ea…

Many protein systems fold in a two-state manner. Random models, however, rarely display two-state kinetics and thus such behavior should not be accepted as a default. While theories for the prevalence of two-state kinetics have been presented, none sufficiently explain the breadth of experimental observations. A model, making minimal assumptions, is introduced…

This Perspective presents a personal overview of the current status of the theory of chemical kinetics and mechanisms for complex processes. We attempt to assess the status of the field for reactions in the gas phase, at gas-solid interfaces, in liquid solutions, in enzymes, and for protein folding. Some unifying concepts such as potential energy surfaces, fre…

PMID:24297278 | DOI:Read more

The folding mechanism of the N-terminal domain of ribosomal protein L9 (NTL91-39) is studied using temperature-jump (T-jump) amide I’ two-dimensional infrared (2D IR) spectroscopy in combination with spectral simulations based on a Markov state model (MSM) built from millisecond-long molecular dynamics trajectories. The results provide evidence for a compact w…

Markov state models provide a powerful framework for the analysis of biomolecular conformation dynamics in terms of their metastable states and transition rates. These models provide both a quantitative and comprehensible description of the long-time scale dynamics of large molecular dynamics with a Master equation and have been successfully used to study prot…

Developing an understanding of protein misfolding processes presents a crucial challenge for unlocking the mysteries of human disease. In this article, we present our observations of β-sheet-rich misfolded states on a number of protein dynamical landscapes investigated through molecular dynamics simulation and Markov state models. We employ a nonequilibri…

The B1 domain of protein G has been a classic model system of folding for decades, the subject of numerous experimental and computational studies. Most of the experimental work has focused on whether the protein folds via an intermediate, but the evidence is mostly limited to relatively slow kinetic observations with a few structural probes. In this work we ob…