Folding of four fast-folding proteins, including chignolin, Trp-cage, villin headpiece and WW domain, was simulated via accelerated molecular dynamics (aMD). In comparison with hundred-of-microsecond timescale conventional molecular dynamics (cMD) simulations performed on the Anton supercomputer, aMD captured complete folding of the four proteins in significantly shorter simulation time. The folded protein conformations were found within 0.2–2.1 Å of the native NMR or X-ray crystal structures. Free energy profiles calculated through improved reweighting of the aMD simulations using cumulant expansion to the 2nd order are in good agreement with those obtained from cMD simulations. This allows us to identify distinct conformational states (e.g., unfolded and intermediate) other than the native structure and the protein folding energy barriers. Detailed analysis of protein secondary structures and local key residue interactions provided important insights into the protein folding pathways. Furthermore, the selections of force fields and aMD simulation parameters are discussed in detail. Our work shows usefulness and accuracy of aMD in studying protein folding, providing basic references in using aMD in future protein-folding studies.
We performed molecular dynamics simulations on systems containing phosphatidycholine headgroups attached to graphene plates (PC-headgroup plates) immersed in water to study the interaction between phosphatidylcholine bilayers in water. The potential of mean force (PMF) between PC-headgroup plates shows that the interaction is repulsive. We observed three distinct regimes in the PMF depending on the interplate distances: the small distance regime, intermediate distance regime, and large distance regime. We believe that the repulsive interaction in the intermediate interplate distance regime is associated with the hydration force due to the removal of water molecules adjacent to the headgroups.
We study models of two sequential enzyme-catalyzed reactions as a basic functional building block for coupled biochemical networks. We investigate the influence of enzyme distributions and long-range molecular interactions on reaction kinetics, which have been exploited in biological systems to maximize metabolic efficiency and signaling effects. Specifically, we examine how the maximal rate of product generation in a series of sequential reactions is dependent on the enzyme distribution and the electrostatic composition of its participant enzymes and substrates. We find that close proximity between enzymes does not guarantee optimal reaction rates, as the benefit of decreasing enzyme separation is countered by the volume excluded by adjacent enzymes. We further quantify the extent to which the electrostatic potential increases the efficiency of transferring substrate between enzymes, which supports the existence of electrostatic channeling in nature. Here, a major finding is that the role of attractive electrostatic interactions in confining intermediate substrates in the vicinity of the enzymes can contribute more to net reactive throughput than the directional properties of the electrostatic fields. These findings shed light on the interplay of long-range interactions and enzyme distributions in coupled enzyme-catalyzed reactions, and their influence on signaling in biological systems.
We used molecular dynamics computer simulations to study the character of interactions between two nanoscale graphene plates in water and also between plates made of "carbon" atoms that have different interaction strength with water. Fluctuations in the number of water molecules in the confined space between plates are qualitatively similar when the plates are made of graphene or when the plates contain "carbon" atoms with weaker "carbon"-water interaction strength. We also observed that these fluctuations are strongly enhanced compared to the fluctuations observed next to a single plate. If the character of water fluctuations in the confined space determines the character of interactions, then it is possible to conclude that the interaction between graphene plates in water is hydrophobic.
Folding of four fast‐folding proteins, including chignolin, Trp‐cage, villin headpiece, and WW domain, was simulated via accelerated molecular dynamics (aMD). Free energy profiles calculated through improved reweighting of the aMD simulations using cumulant expansion to the second‐order are in good agreement with those obtained from long‐timescale conventional molecular dynamics simulations. This work demonstrates the enhanced sampling power of aMD on protein folding and will provide basic references in using aMD for further studies.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.