Molecular Information Theory Meets Protein Folding

J Phys Chem B. 2022 Nov 3;126(43):8655-8668. doi: 10.1021/acs.jpcb.2c04532. Epub 2022 Oct 25.

Abstract

We propose an application of molecular information theory to analyze the folding of single domain proteins. We analyze results from various areas of protein science, such as sequence-based potentials, reduced amino acid alphabets, backbone configurational entropy, secondary structure content, residue burial layers, and mutational studies of protein stability changes. We found that the average information contained in the sequences of evolved proteins is very close to the average information needed to specify a fold ∼2.2 ± 0.3 bits/(site·operation). The effective alphabet size in evolved proteins equals the effective number of conformations of a residue in the compact unfolded state at around 5. We calculated an energy-to-information conversion efficiency upon folding of around 50%, lower than the theoretical limit of 70%, but much higher than human-built macroscopic machines. We propose a simple mapping between molecular information theory and energy landscape theory and explore the connections between sequence evolution, configurational entropy, and the energetics of protein folding.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Entropy
  • Humans
  • Information Theory*
  • Protein Conformation
  • Protein Folding*
  • Protein Structure, Secondary
  • Proteins / chemistry

Substances

  • Proteins