Secondary structure analysis

Table 4 Secondary structure analysis a comparison of resilin-like polypeptides...

The assignment and secondary structure analysis procedure has been carried out for RpIII as well, with overall very similar results. It is clear that basic structural elements of the four strand sheet, and the -turn, are also present. However, we see several extra cross peaks which indicate that there are differences in the segment containing residues 17-19, which will be discussed further below. 

Olafson RW, WD McCubbin, CM Kay (1988) Primary- and secondary-structural analysis of a unique prokaryotic metallothionein from a Synechococcus sp. cyanobacterium. Biochem J 251 691-699. 

J. Xiao, B. Weisbium, P. Wipf, Electrostatic versus steric effects in peptidomimicry Synthesis and secondary structure analysis of gramicidin S analogues with ( )-alkene peptide isosteres, J. Am. Chem. Soc. 127 (2005) 5742-5743. 

Infrared spectroscopy has been an important part of peptide structural analysis for 50 years now. From a rather basic beginning, applications have blossomed to encompass secondary structure analysis, polarization phenomena, membrane conformation, and orientation, and have extended to time-dependent conformational folding mechanisms. Questions have evolved from basic polymer chemistry to issues centered on peptides involved in socially... 

Several analyses can be performed once the full simulation method has been completed. One of the most useful is secondary structure analysis using do dssp. This program, in combination with the xpm2ps program, uses the Dictionary... 

Choice of Basis Sets for the Secondary Structure Analysis of Proteins... 

The simplicity of performing this protein secondary structure analysis makes CD spectroscopy useM in monitoring protein conformational changes between wild-type and mutant proteins, as well as in identifying changes in the protein secondary structure upon addition of a bound cofactor such as a metal ion. Several recent examples of applying CD spectroscopy for these purposes are now described. 

Two types of secondary structure analysis were used on the spectra collected in this study. The classic curve-fitting method (13) for analysis of the amide I band, was performed in two stages. The first step in the analysis is band narrowing, which allows visualization of component bands, using derivatization and Fourier self-deconvolution (FSD) (14). 

It has been shown here that ATR-FTIR spectra of proteins in solution can be collected and used successfully for secondary structural analysis. Relatively accurate bulk protein spectra can be obtained by subtracting the spectrum of protein irreversibly adsorbed to the surface of an IRE. 

Vis, H., Boelens, R., Mariani, M., Stroop, R., Vorgias, C. E., Wilson, K. S., Kaptein, R. (1994). H, C, and N resonance assignments and secondary structure analysis of the HU protein from Bacillus stearothermophilus using two-and three-dimensional double- and triple-resonance heteronuclear magnetic resonance spectroscopy. Biochemistry 33, 14858-14870. 

Caughey BW, Dong A, Bhat KS et al (1991) Secondary structure analysis of the scrapie-associated protein PrP 27-30 in water by infrared spectroscopy. Biochemistry 30 7672-7680... 

Ahmed A, Tajmir-Riahi HA, Carpentier R. A quantitative secondary structure analysis of the 33 kDa extrinsic polypeptide of photosystem II by FTIR spectroscopy. FEBS Lett 1995 363 65-68. 

Because nearly all currently used methods for secondary structural analysis by CD use crystal structure data, two concerns need to be addressed. Are protein structures the same in solution as they are in the crystal In a few specific cases, significant differences have been proposed on the basis of CD or VCD. The most definitive comparisons of solution versus crystal structure are provided by multidimensional NMR studies, which can yield solution structures for small proteins (< 20 kDa), comparable in accuracy to those from X-ray diffraction. One review concludes that, in most cases, the solution and crystal structures are very similar, allowing for some differences in the local conformation and dynamics of surface residues. In a few cases, distinct differences have been demon-... 

Thus, developments in secondary structural analysis from CD have substantially improved the accuracy of the method. For a helix, there has been little improvement, but even the early methods gave rather good estimates of helix content. Estimates of j8-sheet, j8-turn, and other structural contents have shown the greatest improvement. 

Johnson and Gray have applied their method of analysis to the secondary structure of Escherichia coli 5 S RNA, an RNA for which several secondary structural models have been proposed, based on extensive sequence data. The results were in good agreement with two of the proposed models but showed substantial differences with two other models. Thus, this method of secondary structure analysis for RNA can provide a test for proposed models based on sequence analysis. 

G. A. Arteca, O. Nilsson, and O. Tapia,/. Mol. Graphics, 11,193 (1993). Global Characterization of Protein Secondary Structures. Analysis of Computer-Modeled Protein Unfolding. 

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