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Position dependence of the 13 C chemical shifts of α‐helical model peptides. Fingerprint of the 20 naturally occurring amino acids
Author(s) -
Vila Jorge A.,
Baldoni Héctor A.,
Scheraga Harold A.
Publication year - 2004
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.04930804
Subject(s) - chemical shift , chemistry , amino acid , crystallography , chemical composition , quantum chemical , stereochemistry , molecule , biochemistry , organic chemistry
The position dependence of the 13 C chemical shifts was investigated at the density functional level for α‐helical model peptides represented by the sequence Ac‐(Ala) i ‐X‐(Ala) j ‐NH 2 , where X represents any of the 20 naturally occurring amino acids, with 0 ≤ i ≤ 8 and i + j = 8. Adoption of the locally dense basis approach for the quantum chemical calculations enabled us to reduce the length of the chemical‐shift calculations while maintaining good accuracy of the results. For the 20 naturally occurring amino acids in α‐helices, there is (1) significant variability of the computed 13 C shielding as a function of both the guest residue (X) and the position along the sequence; for example, at the N terminus, the 13 C α and 13 C β shieldings exhibit a uniform pattern of variation with respect to both the central or the C‐terminal positions; (2) good agreement between computed and observed 13 C α and 13 C β chemical shifts in the interior of the helix, with correlation coefficients of 0.98 and 0.99, respectively; for 13 C α chemical shifts, computed in the middle of the helix, only five residues, namely Asn, Asp, Ser, Thr, and Leu, exhibit chemical shifts beyond the observed standard deviation; and (3) better agreement for four of these residues (Asn, Asp, Ser, and Thr) only for the computed values of the 13 C α chemical shifts at the N terminus. The results indicate that 13 C β , but not 13 C β , chemical shifts are sensitive enough to reflect the propensities of some amino acids for specific positions within an α‐helix, relative to the N and C termini of peptides and proteins.