Molecular dynamics simulation of the effect of heat on the conformation of bovine β-lactoglobulin A: A comparison of conventional and accelerated methods

Three molecular dynamics (MD) simulation methods are used to follow the thermal unfolding of bovine β-lactoglobulin (β-lac). The methods used, classical MD simulation at different temperatures in the range 300–500 K, essential dynamics and replica exchange MD, were chosen to give a range of conventional and accelerated methods. At 350 K, just above the experimentally determined denaturation temperature of β-lac only small changes to the tertiary fold and secondary structure were seen during a 110 ns simulation. At 400 K and 450 K more unfolding was observed, but it was not until the temperature was increased to 500 K that substantial disruption to the protein structure was seen. For the time that the heated simulated β-lac molecules occupy the same conformation space, they appear to follow similar unfolding pathways. ED simulations biased along the first 5 eigenvectors (determined at 350 K) give rise to conformations that have a more elongated tertiary fold compared to heated simulations, and do not follow similar unfolding pathways to the heated simulations. The REMD simulation, which is the equivalent of an approximately 0.7 μs simulation at 350 K, shows a small degree of tertiary structure unfolding, but very little secondary structure change. The results are discussed in terms of the structural changes that have been observed to occur experimentally in β-lac.

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► Three methods for simulating the heat denaturation of β-lactoglobulin are compared.
► Essential modes of unfolding are identified using principle component analysis.
► Unfolding starts at the chain ends and in random coil regions between β-strands.
► Simulations heated at high temperature unfold via similar pathways.
► Essential dynamics simulation leads to elongated unfolded conformations.