Computation and Analysis of Protein Circular Dichroism Spectra

Circular Dichroism and Its Application to the Study of Biomolecules

“…The reference or basis curves obtained from linear regression, SVD, or CCA will depend strongly on the proteins included in the data set and an inadequate representation of the spectrum of the unknown will result in a failed analysis (Sreerama and Woody, 2004a).…”

“…Starting from a large database of reference proteins the program sequentially eliminates one or more spectra to create a large series of new databases. SVD is used on these reduced data sets to evaluate the unknown conformation; all the results are then examined and those fulfilling certain selection criteria (see Sreerama and Woody, 2004a) for a good fit are averaged. The two other approaches for introducing variable selection with SVD are known as the minimal basis and locally linearized approaches.…”

“…The latter authors have shown that the data sets available with the CDPro package do perform reasonably well and that this performance is improved still further by including membrane proteins in the reference set. Finally, methods available for obtaining additional structural information by calculating the number of secondary structure segments in a protein and identifying its tertiary structure class have been described (see Sreerama and Woody (2004a) and references therein).…”

“…Chromophores that contribute to protein CD (see below) are generally achiral because they have a plane of symmetry. It is the interaction between the chromophores in the chiral field of the protein that introduces the perturbations leading to optical activity (Sreerama and Woody, 2004a). The near-UV CD bands of proteins (310 -255 nm) derive from Trp, Tyr, Phe, and cystine (Note: cysteine does not absorb in this region) and reflect the tertiary, and occasionally quaternary, structure of the protein.…”

Optimisation of expression and purification of the feline and primate foamy virus transmembrane envelope proteins using a 96 deep well screen

“…The GST fusion proteins of the TM protein of FFV and PFV, purified by NI-NTA affinity purification, were subjected to gel filtration in a Superdex 200 10/300 GL column (GE Healthcare, Germany) equilibrated with gel filtration buffer (PBS, 0.1% sarkosyl, For estimation of secondary structures, CD data were analysed with SELCON3, CDSSTR and CONTINLL programs which are part of the CDpro software package [21,22] using the SMP56 protein reference set which includes spectra of 40 soluble and 13 membrane proteins and which is optimised for interpretation of spectra in the range of 190-240 nm [23,24]. Amino acid based secondary structure predictions were obtained with the PROFsec algorithm included in the PredictProtein package [25].…”