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

Mohammad Reza Ejtehadi | Zendy; S. P. Avall | Zendy; Steven S. Plotkin | Zendy

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

Author(s) -

Mohammad Reza Ejtehadi,

S. P. Avall,

Steven S. Plotkin

Publication year - 2004

Publication title -

proceedings of the national academy of sciences

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 5.011

H-Index - 771

eISSN - 1091-6490

pISSN - 0027-8424

DOI - 10.1073/pnas.0403486101

Subject(s) - downhill folding , protein folding , contact order , lattice protein , chemistry , pairwise comparison , molecular dynamics , folding (dsp implementation) , biological system , chemical physics , statistical physics , biophysics , phi value analysis , physics , computer science , computational chemistry , biology , biochemistry , electrical engineering , engineering , artificial intelligence

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 Calpha-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 phi 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 approximately 20%, and (iii) a considerably larger amount of three-body energy present in chymotripsin inhibitor than in the other proteins studied.

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