The inherent flexibility of peptides and protein fragments quantitized by CD in conjunction with CCA+.
ECD spectroscopy is traditionally used for rapid, non-atomic level structure analysis of natural products such as peptides and proteins. Unlike globular proteins, peptides less frequently adopt a single 3D-fold in a time average manner. Moreover, they exhibit an ensemble of conformers composed of a multitude of substantially different structures. In principle, both ECD- and vibrational circular dichroism (VCD)-spectroscopy are sensitive enough to pick up structural information on these dynamic ensembles. However, the interpretation of the raw spectral data of these highly dynamic molecular systems can be cumbersome. The herein presented Convex Constraint Analysis Plus method, or CCA+ for short (http://www.chem.elte.hu/departments/protnmr/cca/), provides a unique opportunity for spectral ensemble analysis of peptides, glycopeptides, peptidomimetics, and other foldamers. The precision and accuracy of the approach is presented here through different peptide model systems. An interesting temperature and pH dependent folding and unfolding of a miniprotein (e.g. Tc5b variant) is also described. Analysis of CD spectra sets strongly affected by solvent and ion type is also introduced to account for severe environmental-induced structure influencing effect(s). The deconvolution makes always possible the quantitative data analysis even when the interpretation of the deconvolution resulted in pure CD curves is complex.
Jákli
Imre
I
Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter sétány 1/A, H-1117, Budapest, Hungary.
Perczel
András
A
D000465:Algorithms; D002942:Circular Dichroism / Q000379:methods*; D006863:Hydrogen-Ion Concentration; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D012984:Software; D013696:Temperature
D010455:Peptides; D011506:Proteins