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

Table 2.

Analysis of membrane protein CD spectra using soluble protein reference sets available in CDPro

α β T U
Method Reference set λ (nm) δα rα δβ rβ δT rT δU rU δ r
SELCON3 SP29 184–245a 0.12 0.93 0.17 0.88 0.05 0.65 0.08 0.17 0.11 0.85
SP37 185–240 0.10 0.96 0.13 0.93 0.04 0.70 0.07 0.25 0.09 0.92
SP43 190–240 0.09 0.97 0.13 0.97 0.04 0.64 0.08 0.26 0.09 0.92
SP42b 185–240 0.10 0.96 0.12 0.94 0.04 0.82 0.06 0.35 0.09 0.93
SP48b 190–240 0.08 0.97 0.12 0.98 0.04 0.67 0.07 0.37 0.08 0.93
CONTIL/LL SP29 184–245a 0.17 0.84 0.17 0.82 0.05 0.39 0.07 0.14 0.13 0.82
SP37 185–240 0.10 0.94 0.15 0.81 0.07 0.47 0.10 −0.06 0.11 0.85
SP43 190–240 0.10 0.93 0.10 0.96 0.05 0.52 0.08 0.25 0.09 0.91
SP42b 185–240 0.12 0.92 0.15 0.86 0.05 0.47 0.08 0.17 0.11 0.87
SP48b 190–240 0.10 0.93 0.10 0.97 0.05 0.44 0.07 0.30 0.08 0.91
CDSSTR SP29 184–245a 0.12 0.90 0.16 0.87 0.04 0.69 0.08 0.10 0.11 0.85
SP37 185–240 0.09 0.96 0.14 0.96 0.04 0.76 0.08 0.09 0.09 0.90
SP43 190–240 0.08 0.96 0.10 0.97 0.04 0.64 0.08 0.18 0.08 0.93
SP42b 185–240 0.10 0.95 0.13 0.98 0.06 0.64 0.08 0.18 0.09 0.91
SP48b 190–240 0.08 0.96 0.12 0.99 0.05 0.53 0.08 0.20 0.08 0.92

The results for 13 membrane proteins are summarized in this Table. CDPro software package has three programs for CD analysis (SELCON3, CONTIN/LL, and CDSSTR) and seven reference protein sets. Two of the seven reference protein sets in CDPro correspond to secondary structure assignments that include poly(Pro)II type conformation and were not used in this study. The other five reference protein sets are included in this study (number of reference proteins, NREF, 29 to 48 proteins). The performance indices for each of the secondary structures are given as the RMS deviations and correlation coefficients between the X-ray and the CD predicted fractions (δα, rα, . . .). The fractions of regular and distorted α and β structures from CDPro were combined to obtain α- and β-fractions. Overall, performance indices were calculated as the RMS deviations and correlation coefficients (δ and r) for all four secondary structure fractions collectively.

a Even though SP29 can analyze CD data in the wavelength range 178 to 260 nm, the analysis was performed using the available data in the range 184 to 245 nm.

b SP42 and SP48 were constructed by adding five denatured proteins to SP37 and SP43, respectively (Sreerama et al. 2000).