Alpha helix capping in synthetic model peptides by reciprocal side chain–main chain interactions: Evidence for an N terminal “capping box”

A significant fraction of the amino acids in proteins are alpha helical in conformation. Alpha helices in globular proteins are short, with an average length of about twelve residues, so that residues at the ends of helices make up an important fraction of all helical residues. In the middle of a helix, H‐bonds connect the NH and CO groups of each residue to partners four residues along the chain. At the ends of a helix, the H‐bond potential of the main chain remains unfulfilled, and helix capping interactions involving bonds from polar side chains to the NH or CO of the backbone have been proposed and detected. In a study of synthetic helical peptides, we have found that the sequence Ser‐Glu‐Asp‐Glu stabilizes the alpha helix in a series of helical peptides with consensus sequences. Following the report by Harper and Rose, which identifies SerXaaXaaGlu as a member of a class of common motifs at the N termini of alpha helices in proteins that they refer to as “capping boxes,” we have reexamined the side chain–main chain interactions in a varient sequence using 1H NMR, and find that the postulated reciprocal side chain‐backbone bonding between the first Ser and last Glu side chains and their peptide NH partners can be resolved: Deletion of two residues N terminal to the Ser‐Glu‐Asp‐Glu sequence in these peptides has no effect on the initiation of helical structure, as defined by two‐dimensional (2D) NMR experiments on this variant. Thus the capping box sequence Ser‐Glu‐Asp‐Glu inhibits N terminal fraying of the N terminus of alpha helix in these peptides, and shows the side chain–main chain interactions proposed by Harper and Rose. It thus acts as a helix initiating signal. Since normal a helix cannot propagate beyond the N terminus of this structure, the box acts as a termination signal in this direction as well. © 1994 John Wiley & Sons, Inc.

[1]  P. Bork,et al.  On α-helices terminated by glycine , 1991 .

[2]  Jen-Tsi Yang,et al.  Two-Point Calibration of Circular Dichrometer with d-10-Camphorsulfonic Acid , 1977 .

[3]  Milner-White Ej.  Recurring loop motif in proteins that occurs in right-handed and left-handed forms. Its relationship with alpha-helices and beta-bulge loops. , 1988 .

[4]  A. Fersht,et al.  Effect of alanine versus glycine in α-helices on protein stability , 1992, Nature.

[5]  P. Lyu,et al.  Local effect of glycine substitution in a model helical peptide , 1991 .

[6]  G. Rose,et al.  Helix signals in proteins. , 1988, Science.

[7]  R. L. Baldwin,et al.  Kinetics of amide proton exchange in helical peptides of varying chain lengths. Interpretation by the Lifson-Roig equation. , 1992, Biochemistry.

[8]  J. Richardson,et al.  Amino acid preferences for specific locations at the ends of alpha helices. , 1988, Science.

[9]  B. Forood,et al.  Stabilization of alpha-helical structures in short peptides via end capping. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[10]  N. Kallenbach,et al.  The helix–coil transition in heterogeneous peptides with specific side‐chain interactions: Theory and comparison with CD spectral data , 1991, Biopolymers.

[11]  P. Lyu,et al.  Analysis of Asymmetry in the Distribution of Helical Residues in Peptides by 1H Nuclear Magnetic Resonance , 1991 .

[12]  B. Zimm,et al.  Theory of the Phase Transition between Helix and Random Coil in Polypeptide Chains , 1959 .

[13]  W. DeGrado,et al.  A thermodynamic scale for the helix-forming tendencies of the commonly occurring amino acids. , 1990, Science.

[14]  A. Bax,et al.  Direct identification of relayed nuclear overhauser effects , 1986 .

[15]  L. Pauling,et al.  The structure of proteins; two hydrogen-bonded helical configurations of the polypeptide chain. , 1951, Proceedings of the National Academy of Sciences of the United States of America.

[16]  D. Wemmer,et al.  Solution structure of apamin determined by nuclear magnetic resonance and distance geometry. , 1988, Biochemistry.

[17]  G. Rose,et al.  Helix stop signals in proteins and peptides: the capping box. , 1993, Biochemistry.

[18]  R. Woody.  Chapter 2 – Circular Dichroism of Peptides , 1985 .

[19]  J. Lecomte,et al.  Helix formation in apocytochrome b5: the role of a neutral histidine at the N-cap position , 1991 .

[20]  Pierre Plateau,et al.  Exchangeable proton NMR without base-line distorsion, using new strong-pulse sequences , 1982 .

[21]  G. Fasman.  The Development of the Prediction of Protein Structure , 1989 .

[22]  P. Lyu,et al.  Position-dependent stabilizing effects in .alpha.-helices: N-terminal capping in synthetic model peptides , 1992 .

[23]  P. Bork,et al.  On a-helices terminated by glycine2. Recognition by sequence patterns , 1991 .

[24]  Kurt Wüthrich,et al.  Origin of τ2 and τ2 ridges in 2D NMR spectra and procedures for suppression , 1986 .

[25]  Alan R. Fersht,et al.  Capping and α-helix stability , 1989, Nature.

[26]  Richard R. Ernst,et al.  Elucidation of cross relaxation in liquids by two-dimensional N.M.R. spectroscopy , 1980 .

[27]  C. Dempsey.  pH Dependence of hydrogen exchange from backbone peptide amides of melittin in methanol , 1988 .

[28]  R. L. Baldwin,et al.  Aromatic side-chain contribution to far-ultraviolet circular dichroism of helical peptides and its effect on measurement of helix propensities. , 1993, Biochemistry.

[29]  J. Brandts,et al.  Derivative sspectroscopy applied to tyrosyl chromophores. Studies on ribonuclease, lima bean inhibitors, insulin, and pancreatic trypsin inhibitor. , 1973, Biochemistry.

[30]  N R Kallenbach,et al.  Side chain contributions to the stability of alpha-helical structure in peptides. , 1990, Science.

[31]  P. Lyu,et al.  Capping interactions in isolated alpha helices: position-dependent substitution effects and structure of a serine-capped peptide helix. , 1993, Biochemistry.