Secondary structure characteristics, correlation

The following characteristics of secondary structures may correlate to the sequence preference and subsequent fold of globular proteins ... 

The left-handed Z-DNA structure of poly[d(A-T)] poly[d(A-T)] as well as poly[d(A-C)] poly[d(G-T)] in the presence of Ni ions leads to characteristic IR and Raman spectra. Markers for these particular double-helical secondary structures are Raman frequency (phos-phodiester chain vibration at 746 and 815 cm syn geometry of the purines evidenced by a breathing mode coupled to the deoxyribose vibration at 622 cm a characteristic profile in the 1300-1400 cm region with a shift of the 1374 cm purine line lo lower wavenumbers correlated with the antijsyn reorientation of the nucleosides under the B - Z transition. " ... 

D Correlation Spectroscopy. A simple, quahtative approach has been described for the determination of membrane protein secondary structure and topology in lipid bilayer membranes." The new approach is based on the observation of wheel-like resonance patterns in the NMR H- N/ N polarization inversion with spin exchange at the magic angle (PISEMA) and H/ N HETCOR spectra of membrane proteins in oriented lipid bilayers. These patterns, named Pisa wheels, have been previously shown to reflect helical wheel projections of residues that are characteristic of a-helices associated with membranes. This study extends the analysis of these patterns to P-strands associated with membranes and demonstrates that, as for the case of a-helices, Pisa wheels are extremely sensitive to the tilt, rotation, and twist of P-strands in the membrane and provide a sensitive, visually accessible, qualitative index of membrane protein secondary structure and topology. 

The amide I band region (1620-1680 cm ) can be used to monitor different classes of secondary structure, where absorbance is dominated by C=0 vibrations. Second derivative peaks in this region are characteristic of secondary structure environments (yS-sheet 1638/1628 cm a-helix 1655 cm yS-turn 1686/1679 cm 3io helix 1660 cm ), and correlations between changes in these peaks with time of exposure in D2O can be used to assign exchange rates to various secondary structures, thus improving resolution [66-68]. For example, a recent study of brain-derived neurotrophic factor (BDNF) binding to its receptor (trkB) used... 

In this review isentropic compressibility data have been compiled for aqueous solutions of the amino acids, including all those found in proteins, of various peptides of low molar mass, and of many proteins. For both the small molecule and protein systems, it is clear that this thermodynamic property is a particularly sensitive measure of hydration effects in aqueous solution. For the small solutes attempts have been made to rationalize the compressibility data in terms of the interactions that occur between the various functional groups and solvent water. For proteins it has been shown that the compressibilities are not correlated with any one structural characteristic. Various characteristics such as amino acid composition, hydrophobicity and the degree of secondary structure all influence, to some degree, the compressibility of a protein. Compressibility measurements on protein solutions also provide an important means to determine the volume fluctuation of a protein. We believe that compressibility measurements on aqueous solutions of these biologically important molecules provide a very powerful means of probing and characterizing solute -water interactions in these systems. 

This strongly levorotatory secondary base contains a trisubstituted double bond and, similar to kurchiphylline, exhibits a carbonyl maximum at 1742 cm i in the IR-spectrum. The presence of the 16-keto group was confirmed by the mass spectrum in which the fragments at m/e 298 and m/e 213 were identical with those reported as characteristic 61) of this keto group. The structure LXIX was proved by correlation with hola-mine (3a-aminopregn-5-en-20-one). On Wolff-Kishner reduction acetyl-... 

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