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

@article{citeulike:5092473, abstract = {The position dependence of the (13)C chemical shifts was investigated at the density functional level for alpha-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 < or = i < or = 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 alpha-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(alpha) and (13)C(beta) 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(alpha) and (13)C(beta) chemical shifts in the interior of the helix, with correlation coefficients of 0.98 and 0.99, respectively; for (13)C(alpha) 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(alpha) chemical shifts at the N terminus. The results indicate that (13)C(beta), but not (13)C(beta), chemical shifts are sensitive enough to reflect the propensities of some amino acids for specific positions within an alpha-helix, relative to the N and C termini of peptides and proteins.}, author = {Vila, J. A. and Baldoni, H. A. and Scheraga, H. A.}, citeulike-article-id = {5092473}, citeulike-linkout-0 = {http://dx.doi.org/10.1110/ps.04930804}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/15498939}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=15498939}, doi = {10.1110/ps.04930804}, issn = {0961-8368}, journal = {Protein science : a publication of the Protein Society}, keywords = {13c, alpha-helices, amino\_acid, nmr}, month = {November}, number = {11}, pages = {2939--2948}, posted-at = {2009-07-08 14:28:53}, priority = {2}, title = {Position dependence of the 13C chemical shifts of alpha-helical model peptides. Fingerprint of the 20 naturally occurring amino acids.}, url = {http://dx.doi.org/10.1110/ps.04930804}, volume = {13}, year = {2004} }

TY - JOUR ID - citeulike:5092473 L3 - citeulike-article-id:5092473 N2 - The position dependence of the (13)C chemical shifts was investigated at the density functional level for alpha-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 < or = i < or = 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 alpha-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(alpha) and (13)C(beta) 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(alpha) and (13)C(beta) chemical shifts in the interior of the helix, with correlation coefficients of 0.98 and 0.99, respectively; for (13)C(alpha) 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(alpha) chemical shifts at the N terminus. The results indicate that (13)C(beta), but not (13)C(beta), chemical shifts are sensitive enough to reflect the propensities of some amino acids for specific positions within an alpha-helix, relative to the N and C termini of peptides and proteins. IS - 11 JF - Protein science : a publication of the Protein Society SN - 0961-8368 EP - 2948 TI - Position dependence of the 13C chemical shifts of alpha-helical model peptides. Fingerprint of the 20 naturally occurring amino acids. VL - 13 SP - 2939 KW - 13c KW - alpha-helices KW - amino_acid KW - nmr AU - Vila, JA AU - Baldoni, HA AU - Scheraga, HA PY - 2004/11// UR - http://dx.doi.org/10.1110/ps.04930804 ER -