# Hydrogen-Bond Lengths in Polypeptide Helices: No Evidence for Short Hydrogen Bonds

Aravinda, Subrayashastry and Datta, Saumen and Shamala, Narayanaswamy and Balaram, Padmanabhan (2004) Hydrogen-Bond Lengths in Polypeptide Helices: No Evidence for Short Hydrogen Bonds. In: Angewandte Chemie International Edition, 43 (48). pp. 6728-6731.

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## Abstract

The $3_1_0$ helix and \alpha helix are closely related secondary structures observed in polypeptides. The $3_1_0$ helix is characterized by successive $4\rightarrow1$ $(C_1_0)$ hydrogen bonds ($C_1_0$= 10 atom hydrogen-bonding ring) of the type $C=O_i\cdot\cdot\cdot$ $HN_{i+3},$ while the $\alpha$ helix displays a hydrogen bond of the type $C= O_i\cdot\cdot\cdot$ $HN_{i+4} (C_{13})$ The $\alpha$ helix is widely distributed in proteins, while the occurrence ofsegments of $3_1_0$ helix is very much less frequent. In polypeptides containing $C^{\alpha,\alpha}$ dialkylated residues, $\alpha$-aminoisobutyric acid (Aib) being the prototype, both the $3_1_0$ and a helical structures are detected. In homooligomers ofAib , $3_1_0$ helices are invariably found in crystals,$^[^3^]$ while in heteromeric sequences the precise helical type appears to depend on both Aib content and positioning. While distinctions between $3_1_0$ and \alpha helices are possible in the crystalline state, such differentiation becomes difficult in solution. Circular dichroism (CD) has been proposed for distinguishing between $3_1_0$ and \alpha helix structures by using the ratio of CD bands at 222 nm and 207/208 nm. However, the use of the $[\theta]_{222}/[\theta]_{208}$ ratio has been questioned, suggesting that the distinction between $3_1_0$ and $\alpha$ helix structures by chiroptical methods may not be readily possible. The conventional interpretation ofthe CD spectra of helical polypeptides has been further called into question by the careful work of Kemp and co-workers, who have reported the observation oflarge values of$[\theta]_2_2_2,$ which are inconsistent with those currently accepted for 100% helical structures. Kemp et al. have noted that the 222 nm $n\pi$* band has not been modeled satisfactorily by heory. The widespread use ofthe CD band intensities at 208 and 222 nm, in estimating helicity values quantitatively and in making qualitative distinctions between helix subtypes, underscores the importance importance ofrelating CD spectral intensities to specific peptide structural features. In addressing this issue, Dang and Hirst have used an improved theoretical method to calculate the 220 nm CD band intensities and have suggested that $[\theta]_2_2_0$ is extremely sensitive to main-chain hydrogen-bond length. They argue that “shortening from a conventional oxygen– nitrogen separation ofabout $3.0 \AA \hspace {2mm}to \hspace {2mm} 2.8 \AA \hspace {2mm} or \hspace {2mm}2.7 \AA$ is predicted to lead to a sizable enhancement of the intensity at 220 nm, with the effect being most pronounced for \alpha helices and less dramatic for $3_1_0$ and \pi helices. These calculations also reveal a dependence of$[\theta]_2_2_0_{nm}$ on ${N\cdot\cdot\cdot$O} separations in the range $3.0-3.5 \AA,$ a factor which may contribute to the variations in band intensities in model $3_1_0$ and $\alpha$ helical peptides. With the exception ofthe Dang and Hirst proposal no testable explanations have been advanced for the observed variation in the 220 nm CD band intensity.

Item Type: Journal Article The copyright of this article belongs to Wiley-VCH Verlag GmbH & Co. circular dichroism;helical structures;hydrogen bonds;peptides;structure elucidation Division of Biological Sciences > Molecular Biophysics UnitDivision of Physical & Mathematical Sciences > Physics 25 Aug 2008 19 Sep 2010 04:24 http://eprints.iisc.ernet.in/id/eprint/5793