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Arginine side chain stacking with peptide plane stabilizes the protein helix conformation in a cooperative way
Author(s) -
Wang Jia,
Chen Jingfei,
Li Jingwen,
An Liaoyuan,
Wang Yefei,
Huang Qingshan,
Yao Lishan
Publication year - 2018
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.25495
Subject(s) - stacking , cooperativity , side chain , crystallography , chemistry , protein structure , protein data bank (rcsb pdb) , helix (gastropod) , peptide bond , electrostatics , alpha helix , peptide , stereochemistry , circular dichroism , biochemistry , organic chemistry , ecology , snail , biology , polymer
Abstract A combined experimental and computational study is performed for arginine side chain stacking with the protein α‐helix. Theremostability measurements of Aristaless homeodomain, a helical protein, suggest that mutating the arginine residue R106, R137 or R141, which has the guanidino side chain stacking with the peptide plane, to alanine, destabilizes the protein. The R‐PP stacking has an energy of ∼0.2‐0.4 kcal/mol. This stacking interaction mainly comes from dispersion and electrostatics, based on MP2 calculations with the energy decomposition analysis. The calculations also suggest that the stacking stabilizes 2 backbone‐backbone h‐bonds ( i → i ‐4 and i ‐3→ i ‐7) in a cooperative way. Desolvation and electrostatic polarization are responsible for cooperativity with the i → i ‐4 and i ‐3→ i ‐7 h‐bonds, respectively. This cooperativity is supported by a protein α‐helices h‐bond survey in the pdb databank where stacking shortens the corresponding h‐bond distances.