Peptides random coil

These features are characteristic of peptide random coil and p-sheet structures, and the magnitude of the positive ellipticity band revealed a significant difference in p-sheet contents between the two toxins. The secondary structures of the two toxins were found to be disrupted by the addition of 5.2 M guanidine hydrochloride at pH 7.4, since the spectra changed to a pattern typical of predominantly random coil structure. It was concluded that co-[d-Ser ]Aga-TK has a significantly higher p-sheet content than co-[l-Ser 6]Aga XK under neutral conditions. 

As a prelude to our binding studies, the secondary structure of aPNA itself was examined using CD spectroscopy [52]. The first aPNA to be studied was the tail-to-tail bl dimer, [Ac-Cys-Gly-Ser -Asp-Ala-Glu-Ser -Ala-Ala-Lys-Ser -Ala-Ala-Glu-Ser -Ala-Aib-Ala-Ser -Lys-Gly-NH2]2- The far-UV CD spectra of this aPNA in water at 30 °C showed the double minimum at 220 nm (n-n transition) and 206 nm (n-n transition) as well as the maximum at 193 nm (n-n transition), characteristic of a peptide a-hehx. Upon increasing the temperature, the intensity of the minimum at 200 nm decreased indicating a transition from a-helix to random stracture. An isodichroic point at 202 nm was suggestive of a temperature-depen-dent a-helix to random coil transition. The helical content of this T5(bl)-dimer at 20°C in water was estimated to be 26% [40]. 

Next, the CD spectra of the backbone 2 aPNA Ac-Cys -Lys-Ser -Ala-Ala-Lys-Ser -Ala-Ala-Lys-SerhAla-Ala-Lys-Ser -Ala-Ala-Lys-Ser -Gly-Lys-NH2, was measured as a function of pH in phosphate buffer. At pH 7, the secondary structure of this aPNA was largely random coil. However, the a-hehcity of this aPNA increased with the pH until it reached a maximum at pH 11. Analogous pH-depen-dent secondary structure has also been reported for the amphipathic KALA peptide Trp-Glu-Ala-Lys-Leu-Ala-[Lys-Ala-Leu-Ala]2-Lys-His-Leu-Ala-Lys-Ala-Leu-Ala-Lys-Ala-Leue-Lys-Ala-Cys-Glu-Ala-OH [53]. In our case however, maximum a-helicity... 

These studies showed thaL in the absence of nucleic acid, the backbone 1 aPNA had significant a-hehcal content at pH 7 whereas the backbone 2 aPNA was largely in a random coil conformation at physiological pH. The latter aPNA did become a-helical at higher pHs in a manner reminiscent of the structurally related amphipathic peptides. 

These free energies determine the critical concentrations for observing each peptide structure. In very dilute conditions, this class of peptides exist as random coil monomers in conformational flux. Above a critical concentration, C( pg, the concentration of monomer remains constant and formation of tapes occurs ... 

Figure 11a shows a force-distance profile measnred for poly(L-glutamic acid) brushes (2C18PLGA(44)) in water (pH = 3.0, 10 M HNO3) deposited at 40 mN/m from the water subphase at pH = 3.0. The majority of peptides are in the forms of an a-helix (38% determined from the amide I band) and a random coil. Two major regions are clearly seen in... 

Altschuler EL, Hud NY, Mazrimas JA, Rupp B. Random coil conformation for extended polyglutamine stretches in aqueous soluble monomeric peptides. J Peptide Res 1997 50 73-75. 

The random coil amide I VCD pattern is exacdy the same shape, but smaller in amplitude and shifted in frequency from the pattern characteristic of poly-L-proline II (PLP II) which is a left-handed 3ihelix of trans peptides (Kobrinskaya et al., 1988 Dukor and Keiderling, 1991 Dukor et al., 1991 Dukor and Keiderling, 1996 Keiderling et al., 1999b). This... 

Fig. 4. Amide f FTIR (top) and VCD (bottom) of thermally further unfolded random coil peptide, oligo-L-lysine, at 5°C (solid line), 50°C (dashed) and 75°C (dash-dot). Low temperature results reflect the polymer spectrum (Fig. 2, bottom), but with somewhat reduced intensity. Higher temperatures result in an IR frequency shift and loss of VCD amplitude, indicating a loss of structure. Measured amplitudes shown. Reprinted from Keiderling, T. A., Silva, R. A. G. D., Yoder, G., and Dukor, R. K. (1999b). Bioorg. Med. Chem. 7, 133-141. 1999, with permission from Elsevier Science.

Fig. 6. Spectral monitoring of the thermal denaturation of the highly helical, Ala-rich peptide Ac-(AAAAK)3AAAA-YNH2 in D20 from 5 to 60°C, as followed by changes in the amide V IR (left) and VCD (right). IR show a clear shift to higher wavenumber from the dominant a-helical peak (here at an unusually low value, 1637 cm-1, due to full solvation of the helix) to a typical random coil value ( 1645 cm-1). VCD loses the (—,+,—) low-temperature helical pattern to yield a broad negative couplet, characteristic of a disordered coil, at high temperature. Spectra were normalized to A = 1.0 by 45°C.

Thermally denatured proteins have been studied for a variety of systems using FTIR and VCD. The resulting high-temperature spectra often reflect the characteristics seen earlier for random coil peptides as well as that seen for the unstructured casein. Particularly the amide I IR bands show a frequency shift to center on a broadened band at 1645-50 cm-1. The amide I VCD loses its distinctive character (Fig. 11) and tends toward... 

It is common today to consider a peptide or an unfolded protein to be random coil —i.e., a blend of conformations—if their CD spectra resemble the traditionally accepted random coil CD spectrum (Blanco and Serrano, 1995 Dyson et al., 1992 Jimenez et al., 1993 Luisi et al., 1999 Munoz et al., 1995 Najbar et al., 2000 Viguera etal., 1996). As we argue here, this CD spectrum does not correspond to random coil at all. Theoretical calculated spectra representing blends of different conformations have been published by Krimm s group (Ronish and Krimm, 1972, 1974). While the results are uncertain because of the unknown compositional coefficients for each conformation in the blend, these spectra are clearly unrelated to that of Pn and many unfolded peptides and proteins. We need to reconsider what kind of CD spectrum is an appropriate representative for a true random coil. 

Nilsson KPR, Rydberg J, Baltzer L, Inganas O (2004) Twisting macromolecular chains self-assembly of a chiral supermolecule from nonchiral polythiophene polyanions and random-coil synthetic peptides. Proc Natl Acad Sci USA 101 11197-11202... 

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