Journal Article

Validation of DBFOLD: An efficient algorithm for computing folding pathways of complex proteins

Jacobs, William M., Bitran, Amir, Shakhnovich, Eugene

2020

Overview

Atomistic simulations can provide valuable, experimentally-verifiable insights into protein folding mechanisms, but existing ab initio simulation methods are restricted to only the smallest proteins due to severe computational speed limits. The folding of larger proteins has been studied using native-centric potential functions, but such models omit the potentially crucial role of non-native interactions. Here, we present an algorithm, entitled DBFOLD, which can predict folding pathways for a wide range of proteins while accounting for the effects of non-native contacts. In addition, DBFOLD can predict the relative rates of different transitions within a protein’s folding pathway. To accomplish this, rather than directly simulating folding, our method combines equilibrium Monte-Carlo simulations, which deploy enhanced sampling, with unfolding simulations at high temperatures. We show that under certain conditions, trajectories from these two types of simulations can be jointly analyzed to compute unknown folding rates from detailed balance. This requires inferring free energies from the equilibrium simulations, and extrapolating transition rates from the unfolding simulations to lower, physiologically-reasonable temperatures at which the native state is marginally stable. As a proof of principle, we show that our method can accurately predict folding pathways and Monte-Carlo rates for the well-characterized Streptococcal protein G. We then show that our method significantly reduces the amount of computation time required to compute the folding pathways of large, misfolding-prone proteins that lie beyond the reach of existing direct simulation. Our algorithm, which is available online , can generate detailed atomistic models of protein folding mechanisms while shedding light on the role of non-native intermediates which may crucially affect organismal fitness and are frequently implicated in disease.

• Publisher: Public Library of Science,Public Library of Science (PLoS)
• Subject: Algorithms / Amino acids / Bacterial Proteins - chemistry / Balancing / Biology and Life Sciences / Computational Biology / Computer and Information Sciences / Computer applications / Evaluation / Exchanging / Folding / High temperature / Interactomes / Intermediates / Kinetics / Methods / Molecular dynamics / Molecular Dynamics Simulation - statistics & numerical data / Monte Carlo Method / Monte Carlo simulation / Physical sciences / Protein Conformation / Protein Folding / Protein Unfolding / Proteins / Research and analysis methods / Sampling / Sampling methods / Sampling techniques / Simulation / Software / Structure / Technology application / Temperature / Thermodynamics