Secondary structural analysis of two recombinant murine proteins, interleukins 1.alpha. and 1.beta.: Is infrared spectroscopy sufficient to assign structure?

Abstract

The secondary structure for two murine recombinant proteins, interleukins 1 alpha and 1 beta (rmIL-1 alpha and -1 beta), has been analyzed by Fourier transform infrared (IR) spectroscopy and then compared to results obtained by X-ray diffraction, circular dichroism (CD), and nuclear magnetic resonance (NMR) spectroscopy. The IR results obtained here for rmIL-1 alpha and -1 beta suggested that their secondary structures consisted predominantly of beta-sheets or strands. However, the analysis also revealed a significant absorption band near 1656 cm-1, which is typically assigned to alpha-helical or random structures. When these same murine polypeptides were analyzed by CD, no evidence of alpha-helical structures was observed. Further, published X-ray diffraction and NMR studies characterizing the human forms of IL-1 alpha and -1 beta indicate the absence of alpha-helices and that the human proteins are composed mainly of beta-strands (i.e., greater than 55%), with approximately 24% of the amino acids involved in large loops connecting the strands. The murine IL-1 proteins, when compared to their respective human counterparts, each show greater than 80% sequence homology. Given this fact, the CD analyses, and the result that this IR band amounted to 21% of the overall integrated area, the absorption peak at 1656 cm-1 was attributed to the presence of large loops rather than to alpha-helical or random structures. Such a structural assignment appears reasonable and is totally consistent with the established existence of large loops in the human forms as well as in other proteins found to fold similarly (viz., human bFGF).(ABSTRACT TRUNCATED AT 250 WORDS)

Analysis of the Structural Organization and Thermal Stability of two Spermadhesins

“…SA, trace h). The position of the band rnaxiiiium is typical of proteins containing a high content of [I-sheel structure 122, 37, 3x1 in agreement with our CD analysis (see above). Native structure for both proteins is supporkd by the existence of a residual amirle 11 band (1600-IS00 cm ') due to deutcrium-unaccesible NH groups.…”

“…However, CD studies had shown that the percentage of helical structure was below that value. The overestimation of rr-helix content by FT1R could be due to the appearance of certain deuterated forms of loop structures that have been reported to occur at I656 cm-I [37]. Therefore, loop and helical conformations were considered for such a band.…”

Structural and Thermodynamic Characterization of Pal, a Phage Natural Chimeric Lysin Active against Pneumococci

“…In D 2 O (25), bands centered around 1679 cm Ϫ1 can be assigned to the high frequency component of ␤-sheets, whose intensity would be less than one-tenth of the low frequency component that appears around 1630 cm Ϫ1 , and bands centered near 1671 cm Ϫ1 have been associated to ␤-turns. The band about 1652 cm Ϫ1 is usually produced by ␣-helix, although bands originated from large loops have also been described around this frequency (26,27). Finally, bands centered at about 1645 cm Ϫ1 are characteristic of unordered segments.…”

Structural Characterization of the C2 Domains of Classical Isozymes of Protein Kinase C and Novel Protein Kinase Cε by using Infrared Spectroscopy

“…This wavelength can be attributed to β-sheet structure [31], the major structural component of C2 domains [11,26]. The component at 1658 cm −1 , which amounted to 18%, is usually assigned to α-helix and/or unordered structures [28] but could also be assigned to large loops with dihedral angles similar to those of α-helix [7,53,54,57]. The component at 1671 cm −1 , amounting to 22%, is assigned to β-turns [20,21].…”

“…Another possibility is that this part of the domain adopts a helical conformation similar to that of cPLA2-CBR1, which is involved in membrane interaction [44]. Thus, one of those structures may be the origin of the extra helical component found in the IR spectrum of PKCε-C2 domain at 1651 and 1658 cm −1 , in D 2 O and H 2 O, respectively, since both α-helix and large loops appear together at those frequencies [7,28,53,54].…”