Predicting and Understanding the Enzymatic Inhibition of Human Peroxiredoxin 5 by 4-Substituted Pyrocatechols by Combining Funnel Metadynamics, Solution NMR, and Steady-State Kinetics

Metadynamics to Enhance Sampling in Biomolecular Simulations

Molecular dynamics is a powerful simulation method to provide detailed atomic-scale insight into a range of biological processes including protein folding, biochemical reactions, ligand binding, and many others. Over the last several decades, enhanced sampling methods have been developed to address the large separation in time scales between a molecular dynamics simulation (usually microseconds or shorter) and the time scales of biological processes (often orders of magnitude longer). This chapter specifically focuses on the metadynamics family of methods, which achieves enhanced sampling through the introduction of a history-dependent bias potential that is based on one or more slow degrees of freedom, called collective variables. We introduce the method and its recent variants related to biomolecular studies and then discuss frontier areas of the method. A large part of this chapter is devoted to helping new users of the method understand how to choose metadynamics parameters properly and apply the method to their system of interest.

Cancer-Associated Function of 2-Cys Peroxiredoxin Subtypes as a Survival Gatekeeper

Cancer cells are abnormal cells that do not comply with tissue homeostasis but undergo uncontrolled proliferation. Such abnormality is driven mostly by somatic mutations on oncogenes and tumor suppressors. Cancerous mutations show intra-tumoral heterogeneity across cancer types and eventually converge into the self-activation of proliferative signaling. While transient production of intracellular reactive oxygen species (ROS) is essential for cell signaling, its persistent production is cytotoxic. Thus, cancer cells require increased levels of intracellular ROS for continuous proliferation, but overexpress cellular peroxidase enzymes, such as 2-Cys peroxiredoxins, to maintain ROS homeostasis. However, suppression of 2-Cys peroxiredoxins has also been reported in some metastatic cancers. Hence, the cancer-associated functions of 2-Cys peroxiredoxins must be illuminated in the cellular context. In this review, we describe the distinctive signaling roles of 2-Cys peroxiredoxins beyond their intrinsic ROS-scavenging role in relation to cancer cell death and survival.

Resolving the problem of trapped water in binding cavities: prediction of host-guest binding free energies in the SAMPL5 challenge by funnel metadynamics

The funnel metadynamics method enables rigorous calculation of the potential of mean force along an arbitrary binding path and thereby evaluation of the absolute binding free energy. A problem of such physical paths is that the mechanism characterizing the binding process is not always obvious. In particular, it might involve reorganization of the solvent in the binding site, which is not easily captured with a few geometrically defined collective variables that can be used for biasing. In this paper, we propose and test a simple method to resolve this trapped-water problem by dividing the process into an artificial host-desolvation step and an actual binding step. We show that, under certain circumstances, the contribution from the desolvation step can be calculated without introducing further statistical errors. We apply the method to the problem of predicting host–guest binding free energies in the SAMPL5 blind challenge, using two octa-acid hosts and six guest molecules. For one of the hosts, well-converged results are obtained and the prediction of relative binding free energies is the best among all the SAMPL5 submissions. For the other host, which has a narrower binding pocket, the statistical uncertainties are slightly higher; longer simulations would therefore be needed to obtain conclusive results.