Yanxin Liu, Johan Strümpfer, Peter L. Freddolino, Martin Gruebele, and Klaus Schulten. Structural characterization of λ-repressor folding from all-atom molecular dynamics simulations. Journal of Physical Chemistry Letters, 3:1117-1123, 2012. (PMC: 3377354)

LIU2012 The five-helix bundle $\lambda$-repressor fragment is a fast-folding protein. A length of 80 amino acid residues puts it on the large end among all known microsecond folders and its size poses a computational challenge for molecular dynamics (MD) studies. We simulated the folding of a novel $\lambda$-repressor fast-folding mutant ($\lambda$-HG) in explicit solvent using an all-atom description. By means of a recently developed tempering method, we observed reversible folding and unfolding of $\lambda$-repressor in a 10- microsecond trajectory. The folding kinetics was also investigated through a set of MD simulations run at different temperatures that together covered more than 125 microseconds. The protein was seen to fold into a native-like topology at intermediate temperature and a slow-folding pathway was identified. The simulations suggest new experimental observables for better monitoring the folding process, and a novel mutation expected to accelerate $\lambda$-repressor folding.



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