Predicting the folding pathway of engrailed homeodomain with a probabilistic roadmap enhanced reaction-path algorithm

REMD and umbrella sampling simulations to probe the energy barrier of the folding pathways of engrailed homeodomain

Proteins fold by diverse pathways which depend on the energy barriers involved in reaching different intermediates. There has been a lot of development in the theoretical aspects of protein folding, from force-field to simulation techniques. One such simulation approach is replica exchange molecular dynamics simulation (REMD), which provides an efficient conformational sampling method to understand the events involved in protein folding. In this study, an attempt is made to explore the folding funnel of engrailed homeodomain protein (EnHD) using REMD simulations. EnHD is a 54 residue long helix bundle protein which has a folding time of about 15 μs. The protein was represented using the Amber United atom model in order to reduce the system size which helped to speed up the simulation. Individual replicas were simulated for 1.4-2 μs making cumulative time of more than 100 μs of REMD simulations. Free energy analysis was carried out to understand the folding behavior of EnHD protein. Effects of temperature range and exchange frequency in REMD simulations have been explored. In addition to this, multiple umbrella sampling (US) simulations of a total of 320 ns were also carried out, followed by weighted histogram analysis method (WHAM) to investigate the energy barriers involved during the folding of various intermediates. US studies were also carried on mutational variants of EnHD protein to see effect of the mutations on the folding pathway of the protein. The use of US technique may be helpful for predicting fast folding mutants or protein engineering. The combination of REMD with US may help in understanding the energetics between multiple pathways of fast folding proteins and their mutant counterparts.

Observation of two families of folding pathways of BBL

BBL is an independent folding domain of a large multienzyme complex, 2-oxoglutarate dehydrogenase. The folding mechanism of BBL is under debate between the views of noncooperative downhill-type and classical two-state. Extensive replica exchange molecular dynamics simulations of BBL in explicit solvent have shown some non-two-state behaviors despite no definitive evidence of downhill folding. In this work, we postprocess the replica exchange data using our roadmap-based MaxFlux reaction path algorithm to reveal atomically detailed folding pathways. A connected graph is used to organize and visualize the folding pathways initiated from random coils. High structural and transition heterogeneity is seen in the early stage of folding. Two main parallel folding pathways emerge in the later stage; one path shows that tertiary contact and helix formation develop at different stages of folding, whereas the other path exhibits concurrence of secondary and tertiary structure formation to some extent. Because the native state of BBL is sensitive to experimental conditions, we speculate that the relative predominance of the two pathways may vary with the protein construct and solvent conditions, possibly leading to the seeming discrepancy of experimental results. Our roadmap-based reaction path algorithm is a general tool to extract path information from replica exchange.

Refolding the engrailed homeodomain: structural basis for the accumulation of a folding intermediate

The ultrafast folding pathway of the engrailed homeodomain has been exceptionally well characterized by experiment and simulation. Helices II and III of the three-helix bundle protein form the native helix-turn-helix motif as an on-pathway intermediate within a few microseconds. The slow step is then the proper docking of the helices in approximately 15 mus. However, there is still the unexplained puzzle of why helix docking is relatively slow, which is part of the more general question as to why rearrangements of intermediates occur slowly. To address this problem, we performed 46 all-atom molecular dynamics refolding simulations in explicit water, for a total of 15 micros of simulation time. The simulations started from an intermediate state structure that was generated in an unfolding simulation at 498 K and was then quenched to folding-permissive temperatures. The protein refolded successfully in only one of the 46 simulations, and in that case the refolding pathway mirrored the unfolding pathway at high temperature. In the 45 simulations in which the protein did not fully fold, nonnative salt bridges trapped the protein, which explains why the protein folds relatively slowly from the intermediate state.