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. 2004 Jan;13(1):100–112. doi: 10.1110/ps.03258404

Table 3.

Analysis of membrane protein CD spectra with the membrane protein and combined soluble + membrane protein reference sets

α β T U
Method Reference set δα rα δβ rβ δT rT δU rU δ r
SELCON3 MP13a 0.09 0.94 0.07 0.96 0.04 0.51 0.04 0.51 0.06 0.95
SMP50 0.07 0.97 0.08 0.96 0.03 0.68 0.06 0.25 0.06 0.95
SMP56 0.09 0.94 0.08 0.97 0.04 0.57 0.06 0.29 0.07 0.95
CONTIN/LL MP13a 0.13 0.89 0.07 0.96 0.04 0.48 0.08 0.02 0.09 0.92
SMP50 0.09 0.95 0.07 0.96 0.04 0.62 0.08 −0.01 0.07 0.94
SMP56 0.13 0.88 0.07 0.96 0.05 0.47 0.08 0.12 0.09 0.91
CDSSTR MP13a,b 0.08 0.95 0.06 0.97 0.04 0.54 0.05 0.57 0.06 0.96
SMP50 0.08 0.96 0.08 0.99 0.05 0.75 0.08 0.42 0.08 0.93
SMP56 0.09 0.94 0.08 0.99 0.04 0.64 0.07 0.22 0.07 0.93
Averagec 0.08 0.96 0.09 0.97 0.03 0.71 0.07 0.17 0.07 0.94
CCAd MP30 0.13 0.92 0.17 0.72 0.10 0.50 0.14 0.56 0.14 0.75

The results for 13 membrane proteins are summarized in this table. The membrane protein reference set was constructed with the 13 membrane protein CD spectra (Fig. 1 ▶) and the corresponding secondary structures (Table 1). The combined soluble + membrane protein reference sets were constructed by adding CD spectra and the corresponding secondary structure fractions of 13 membrane proteins to 37- and 43-protein reference sets provided in CDPro forming SMP50 and SMP56, respectively. The wavelength ranges of CD spectra were 185 to 240 nm for MP13 and SMP50 and 190 to 240 for SMP56.

a Each membrane protein in the 13-membrane protein reference set is analyzed by using the other 12 membrane proteins (wavelength range of CD spectra: 185 to 240 nm), and the results are summarized as performance indices.

b The summary for CDSSTR from MP13 includes results for only nine membrane proteins because solutions were not obtained for four membrane proteins (photosystem I, antenna complex, porin [R. capsulatus] and maltoporin).

c Twelve solutions, from three programs (SELCON3, CONTIN/LL, and CDSSTR) and four reference sets (SP37, SP43, SMP50, and SMP56), were averaged.

d CCA results for the 13 membrane protein CD spectra in the wavelength range 184 to 260 nm were taken from Park et al. (1992), obtained with a 30 membrane protein reference set.