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Position dependence of the ¹³C chemical shifts of -helical model peptides. Fingerprint of the 20 naturally occurring amino acids

¹ Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, USA
² Universidad Nacional de San Luis, Facultad de Ciencias Físico, Matemáticas y Naturales, Instituto de Matemática Aplicada San Luis, CONICET, San Luis, Argentina
³ Universidad Nacional de San Luis, Departamento de Química, San Luis, Argentina

(RECEIVED June 12, 2004; FINAL REVISION July 28, 2004; ACCEPTED August 5, 2004)

The position dependence of the ¹³C chemical shifts was investigated at the density functional level for -helical model peptides represented by the sequence Ac-(Ala)_i-X-(Ala)_j-NH₂, 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 -helices, there is (1) significant variability of the computed ¹³C shielding as a function of both the guest residue (X) and the position along the sequence; for example, at the N terminus, the ¹³C and ¹³C 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 ¹³C and ¹³C chemical shifts in the interior of the helix, with correlation coefficients of 0.98 and 0.99, respectively; for ¹³C 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 ¹³C chemical shifts at the N terminus. The results indicate that ¹³C, but not ¹³C, chemical shifts are sensitive enough to reflect the propensities of some amino acids for specific positions within an -helix, relative to the N and C termini of peptides and proteins.

Keywords: ¹³C chemical shifts; -helical peptides; helix breaker; locally dense basis approach

Reprint requests to: Harold A. Scheraga, Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA; e-mail: has5{at}cornell.edu; fax: (607) 254-4700.

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