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Protein folding: could hydrophobic collapse be coupled with hydrogen‐bond formation?
Author(s) -
Fernández Ariel,
Kardos József,
Goto Yuji
Publication year - 2003
Publication title -
febs letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.593
H-Index - 257
eISSN - 1873-3468
pISSN - 0014-5793
DOI - 10.1016/s0014-5793(03)00056-5
Subject(s) - hydrogen bond , chemistry , folding (dsp implementation) , amide , hydrophobic effect , covalent bond , protein folding , lattice protein , crystallography , globular protein , computational chemistry , molecule , organic chemistry , biochemistry , electrical engineering , engineering
A judicious examination of an exhaustive PDB sample of soluble globular proteins of moderate size ( N <102) reveals a commensurable relationship between hydrophobic surface burial and number of backbone hydrogen bonds. An analysis of 50 000 conformations along the longest all‐atom MD trajectory allows us to infer that not only the hydrophobic collapse is concurrent with the formation of backbone amide‐carbonyl hydrogen bonds, they are also dynamically coupled processes. In statistical terms, hydrophobic clustering of the side chains is inevitably conducive to backbone burial and the latter process becomes thermodynamically too costly and kinetically unfeasible without amide‐carbonyl hydrogen‐bond formation. Furthermore, the desolvation of most hydrogen bonds is exhaustive along the pathway, implying that such bonds guide the collapse process.