How long does it take to equilibrate the unfolded state of a protein?

Authors

  • Ronald M. Levy,

    Corresponding author
    1. Department of Chemistry and Chemical Biology, Rutgers, the State University of New Jersey, Piscataway, New Jersey
    • Correspondence to: Levy Ronald, Department of Chemistry and Chemical Biology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854. E-mail: ronlevy@lutece.rutgers.edu

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  • Wei Dai,

    1. Department of Physics and Astronomy, Rutgers, the State University of New Jersey, Piscataway, New Jersey
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  • Nan-Jie Deng,

    1. Department of Chemistry and Chemical Biology, Rutgers, the State University of New Jersey, Piscataway, New Jersey
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  • Dmitrii E. Makarov

    1. Department of Chemistry and Biochemistry and Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas
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Abstract

How long does it take to equilibrate the unfolded state of a protein? The answer to this question has important implications for our understanding of why many small proteins fold with two state kinetics. When the equilibration within the unfolded state U is much faster than the folding, the folding kinetics will be two state even if there are many folding pathways with different barriers. Yet the mean first passage times (MFPTs) between different regions of the unfolded state can be much longer than the folding time. This seems to imply that the equilibration within U is much slower than the folding. In this communication we resolve this paradox. We present a formula for estimating the time to equilibrate the unfolded state of a protein. We also present a formula for the MFPT to any state within U, which is proportional to the average lifetime of that state divided by the state population. This relation is valid when the equilibration within U is very fast as compared with folding as it often is for small proteins. To illustrate the concepts, we apply the formulas to estimate the time to equilibrate the unfolded state of Trp-cage and MFPTs within the unfolded state based on a Markov State Model using an ultra-long 208 microsecond trajectory of the miniprotein to parameterize the model. The time to equilibrate the unfolded state of Trp-cage is ∼100 ns while the typical MFPTs within U are tens of microseconds or longer.

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