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Reduction of the Search Space for the Folding of Proteins at the Level of Formation and Assembly of Secondary Structures: A New View on the Solution of Levinthal′s Paradox
Author(s) -
Finkelstein Alexei V.,
Garbuzynskiy Sergiy O.
Publication year - 2015
Publication title -
chemphyschem
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.016
H-Index - 140
eISSN - 1439-7641
pISSN - 1439-4235
DOI - 10.1002/cphc.201500700
Subject(s) - chemistry , folding (dsp implementation) , protein secondary structure , exponent , protein folding , space (punctuation) , chain (unit) , crystallography , protein structure , chemical physics , physics , biochemistry , computer science , linguistics , philosophy , astronomy , electrical engineering , engineering , operating system
Abstract The complete volume of the protein conformation space is, by many orders of magnitude, smaller at the level of secondary structure elements than that at the level of amino acid residues; the latter, according to Levinthal′s estimate, scales approximately as 10 2 L , with L being the number of residues in the chain, whereas the former, as demonstrated in this paper, scales no faster than ∼ L N , with N being the number of the secondary structure elements, which is approximately equal to L /15. This drastic decrease in the exponent ( L /15 instead of 2 L ) explains why sampling of the conformation space does not contradict the ability of the protein chain to find its most stable fold.