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Structure and disorder in the ribonuclease S‐peptide probed by NMR residual dipolar couplings
Author(s) -
Alexandrescu Andrei T.,
Kammerer Richard A.
Publication year - 2003
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1110/ps.03164403
Subject(s) - residual dipolar coupling , dipole , chemistry , peptide , ribonuclease , anisotropy , dihedral angle , crystallography , protein structure , magnetic dipole–dipole interaction , spins , chemical physics , nuclear magnetic resonance , physics , condensed matter physics , hydrogen bond , rna , molecule , quantum mechanics , biochemistry , organic chemistry , gene
Abstract NMR residual dipolar couplings for the S‐peptide of ribonuclease A aligned in C8E5/ n ‐octanol liquid crystals are consistent with the presence of a native‐like α‐helix structure undergoing dynamic fraying. Residues 3–13, which correspond to the first α‐helix of ribonuclease A, show couplings that become more negative at low temperature and in the presence of salt, conditions which stabilize α‐helical structure in the S‐peptide. By contrast, dipolar couplings from the N and C termini of the peptide are close to zero and remain nearly invariant with changes in solution conditions. Torsion angle dynamics simulations using a gradient of dihedral restraint bounds that increase from the center to the ends of the peptide reproduce the experimentally observed sequence dependence of dipolar couplings. The magnitudes of residual dipolar couplings depend on the anisotropy of the solute. Native proteins often achieve nearly spherical shapes due to the hydrophobic effect. Embryonic partially folded structures such as the S‐peptide α‐helix have an intrinsically greater potential for anisotropy that can result in sizable residual dipolar couplings in the absence of long‐range structure.