Sterics and solvation winnow accessible conformational space for unfolded proteins

Nicholas C. Fitzkee, George D. Rose

Research output: Contribution to journalArticlepeer-review

Abstract

The magnitude of protein conformational space is over-estimated by the traditional random-coil model, in which local steric restrictions arise exclusively from interactions between adjacent chain neighbors. Using a five-state model, we assessed the extent to which steric hindrance and hydrogen bond satisfaction, energetically significant factors, impose additional conformational restrictions on polypeptide chains, beyond adjacent residues. Steric hindrance is repulsive: the distance of closest approach between any two atoms cannot be less than the sum of their van der Waals radii. Hydrogen bond satisfaction is attractive: polar backbone atoms must form hydrogen bonds, either intramolecularly or to solvent water. To gauge the impact of these two factors on the magnitude of conformational space, we systematically enumerated and classified the disfavored conformations that restrict short polyalanyl backbone chains. Applying such restrictions to longer chains, we derived a scaling law to estimate conformational restriction as a function of chain length. Disfavored conformations predicted by the model were tested against experimentally determined structures in the coil library, a non-helix, non-strand subset of the PDB. These disfavored conformations are usually absent from the coil library, and exceptions can be uniformly rationalized.

Original languageEnglish (US)
Pages (from-to)873-887
Number of pages15
JournalJournal of molecular biology
Volume353
Issue number4
DOIs
StatePublished - Nov 4 2005

Keywords

  • Hydrogen-bonding
  • Protein folding
  • Random coil
  • Steric restrictions
  • Unfolded state

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology

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