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Three-body interactions improve the prediction of rate and mechanism in protein folding models

Ejtehadi, M. R ; Sharif University of Technology | 2004

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  1. Type of Document: Article
  2. DOI: 10.1073/pnas.0403486101
  3. Publisher: 2004
  4. Abstract:
  5. Here we study the effects of many-body interactions on rate and mechanism in protein folding by using the results of molecular dynamics simulations on numerous coarse-grained Cα-model single-domain proteins. After adding three-body interactions explicitly as a perturbation to a Gō-like Hamiltonian with native pairwise interactions only, we have found (i) a significantly increased correlation with experimental φ values and folding rates, (ii) a stronger correlation of folding rate with contact order, matching the experimental range in rates when the fraction of three-body energy in the native state is ≈20%, and (iii) a considerably larger amount of three-body energy present in chymotripsin inhibitor than in the other proteins studied
  6. Keywords:
  7. Macromolecular Substances ; Thermodynamics ; Proteins ; Protein Folding ; Plant Proteins ; Peptides ; Molecular ; Models
  8. Source: Proceedings of the National Academy of Sciences of the United States of America ; Volume 101, Issue 42 , 2004 , Pages 15088-15093 ; 00278424 (ISSN)
  9. URL: https://www.pnas.org/doi/full/10.1073/pnas.0403486101