title: Do parallel beta-helix proteins have a unique fourier transform infrared spectrum?
abstract: Several polypeptides have been found to adopt an unusual domain structure known as the parallel beta-helix. These domains are characterized by parallel beta-strands, three of which form a single parallel beta-helix coil, and lead to long, extended beta-sheets. We have used ATR-FTIR (attenuated total reflectance-fourier transform infrared spectroscopy) to analyze the secondary structure of representative examples of this class of protein. Because the three-dimensional structures of parallel beta-helix proteins are unique, we initiated this study to determine if there was a corresponding unique FTIR signal associated with the parallel beta-helix conformation. Analysis of the amide I region, emanating from the carbonyl stretch vibration, reveals a strong absorbance band at 1638 cm(-1) in each of the parallel beta-helix proteins. This band is assigned to the parallel beta-sheet structure. However, components at this frequency are also commonly observed for beta-sheets in many classes of globular proteins. Thus we conclude that there is no unique infrared signature for parallel beta-helix structure. Additional contributions in the 1638 cm(-1) region, and at lower frequencies, were ascribed to hydrogen bonding between the coils in the loop/turn regions and amide side-chain interactions, respectively. A 13-residue peptide that forms fibrils and has been proposed to form beta-helical structure was also examined, and its FTIR spectrum was compared to that of the parallel beta-helix proteins.
authors.affiliation: Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA.
authors.forename: R
authors.initials: R
authors.lastname: Khurana
authors.forename: A L
authors.initials: AL
authors.lastname: Fink
mesh_terms: D000217:Acyltransferases / Q000737:chemistry; D000577:Amides / Q000737:chemistry; D018360:Crystallography, X-Ray; D006026:Glycoside Hydrolases / Q000737:chemistry; D006860:Hydrogen Bonding; D007527:Isoenzymes / Q000737:chemistry; D008958:Models, Molecular; D011133:Polysaccharide-Lyases / Q000737:chemistry; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D017550:Spectroscopy, Fourier Transform Infrared; D017376:Viral Tail Proteins / Q000737:chemistry
chemical_list: D000577:Amides; D007527:Isoenzymes; D017376:Viral Tail Proteins; D000217:Acyltransferases; C050304:acyl-(acyl-carrier-protein)-UDP-N-acetylglucosamine acyltransferase; D006026:Glycoside Hydrolases; C083268:tailspike protein, bacteriophage; D011133:Polysaccharide-Lyases; C023911:pectate lyase