Distinct circular dichroism spectroscopic signatures of polyproline II and unordered secondary structures: Applications in secondary structure analyses

Abstract

Circular dichroism (CD) spectroscopy is a valuable method for defining canonical secondary structure contents of proteins based on empirically-defined spectroscopic signatures derived from proteins with known three-dimensional structures. Many proteins identified as being "Intrinsically Disordered Proteins" have a significant amount of their structure that is neither sheet, helix, nor turn; this type of structure is often classified by CD as "other", "random coil", "unordered", or "disordered". However the "other" category can also include polyproline II (PPII)-type structures, whose spectral properties have not been well-distinguished from those of unordered structures. In this study, synchrotron radiation circular dichroism spectroscopy was used to investigate the spectral properties of collagen and polyproline, which both contain PPII-type structures. Their native spectra were compared as representatives of PPII structures. In addition, their spectra before and after treatment with various conditions to produce unfolded or denatured structures were also compared, with the aim of defining the differences between CD spectra of PPII and disordered structures. We conclude that the spectral features of collagen are more appropriate than those of polyproline for use as the representative spectrum for PPII structures present in typical amino acid-containing proteins, and that the single most characteristic spectroscopic feature distinguishing a PPII structure from a disordered structure is the presence of a positive peak around 220nm in the former but not in the latter. These spectra are now available for inclusion in new reference data sets used for CD analyses of the secondary structures of soluble proteins.

Circular Dichroism Spectroscopy of Collagen Fibrillogenesis: A New Use for an Old Technique

“…This collagen fibril spectrum is distinct from a soluble triple helix and is similar in spectral shape to the polyproline II structure but has a much larger magnitude (Fig. S8) (52,53). This signal is strongly correlated with other measurements of fibrillogenesis, such as rheology and light scattering, and is evident for a number of type-I collagens from diverse source tissues and species.…”

Modular peptides from the thermoplastic squid sucker ring teeth form amyloid-like cross-β supramolecular networks

“…[41,76] A consensus has emerged in the past decade that "disordered" proteins are in fact often dominated by residues that temporally adopt extended (or semi-extended) PII conformations, [39] notably for short peptides. [77,78] For instance NMR studies demonstrated that a 7-residue poly-Ala in aqueous solution adopted a PPII conformation, [40] and similar results were obtained for the penta-peptide GGAGG.…”

Solvation driven conformational transitions in the second transmembrane domain of mycobacteriophage holin

“…Hence, we continued all further analyses in 50 mM phosphate buffer pH 7.2, as it is close to physiological conditions. We examined the effect of detergent concentration on the far-UV CD spectra of TM2, using LDAO (4,10,20,40, and 100 mM) and DPC (5,10,20,30, and 50 mM). In LDAO samples ( Figure 5, top left panel), we observe an increase in the overall ellipticity, which is accompanied by a red shift in the negative maximum from 200 to 204 nm, as the LDAO concentration increases.…”

“…12 It is broadly accepted that PPII structures are observed in poly-L-Pro, poly-L-Glu, poly-L-Lys, and the collagen sequence. 4,[13][14][15] However, segments that adopt PPII-like structures have been observed in short polypeptides and proteins. [16][17][18][19] PPII-like segments with a minimum of length two residues and a maximum of 14 residues has been observed to date.…”

“…5,6 Based on the proline-versus nonproline PPII conformations, CD spectra with different positive and negative maxima are observed, and both structures are widely accepted. 4,37 The conserved Ala-and Gly-rich sequence of TM2 suggests that these residues are essential to dictate the formation of a Pro -PPII-like form in this peptide, under favorable conditions. Environmental factors such as solvent conditions influence the formation of a-helical or PPII-like structures.…”