Peptide, unstructured

An example is shown in Figure 7 for the case of the coil-to-helix transition. The endpoints of the calculation are an unstructured coil Tr and helix rp. Intermediate peptide structures correspond to transition intermediates defining the pathway l(r). 

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... 

These results strongly suggest that unstructured peptides have definite backbone conformations and that the concept of a denatured protein as a structureless random chain breaks down when backbone conformations of individual residues are described, although the random chain concept may still be useful when describing the overall chain conformation. 

The amphipathic a-helical class of host defense peptides is the most abundant and most well-characterized class. Upon interaction with the hydrophobic membrane environment, the largely unstructured peptide adopts an amphipathic ct-helical conformation with one helical face containing the majority of the hydrophobic residues, the opposite containing a large proportion of the polar residues. These peptides are often short (<40 amino acids), devoid of cysteine residues, and found to be unstructured or linear in nonhydrophobic environments. Peptides found within this class include the antimicrobial peptide alamethicin, bee venom melittin, the magainins, and the human cathelicidin LL-37. ... 

As host defense peptides are membrane-active molecules, safety mechanisms must be employed to avoid deleterious contacts with host cells. These mechanisms may involve the limitation of peptide activation to specific environments or niche-specific amplification. That most ct-helical peptides remain unstructured in aqueous solution and undergo conformational transitions to an activated state within hydrophobic environments supports this postulate. It has also been postulated that the order of anionic phospholipids in microbial plasma membranes likely induces optimal periodicity of polar residues within host defense peptides at the membrane surface. ... 

Early investigations of peptides in membrane model systems included studies of mel-letin 124,125 220 221 spectra and polarization properties. This water-soluble peptide is found to be structureless in solution at neutral pH but was sensitive to environmental change. The undecapeptide hormone, substance P, a member of the tackykinin family, was also found by Choo et a].1222 to be unstructured in solution at physiological pH and to aggregate at high pH or on interaction with charged lipids. These data were used as counter-evidence to a hypothesis that the membrane surface structured the peptide to facilitate interaction with the receptor. 

The exchange data could be fit just as well by the CD-derived parameters with a kint about 17% lower than the value used in the fit to exchange rate data alone. In the latter case, /cint was taken to be the same as the rate of exchange observed for an NH group in an unstructured peptide. It is quite plausible that a peptide NH in a partially helical peptide may differ from that in a completely unstructured peptide. Thus, these results indicate that if the CD parameters are carefully determined for the helical and the unordered conformations, the helix content of peptides can be determined accurately, in agreement with alternative measurements by exchange kinetics. 

It is now well established that the 13C chemical shifts of amino acid residues removed more than two units from the chain ends in unstructured polypeptides are not influenced, except by proline moieties, by the peptide sequence (Table 5.27, [96, 791, 792, 802-810]). Chemical shift changes of carbons of the same amino acid at different positions within a peptide or protein are therefore due to effects caused by secondary or tertiary structure. 

ID NMR experiments are often used for quality-control purposes and can readily be used to confirm the purity of peptides. Simple ID spectra are also often used to determine whether a peptide is structured or unstructured or whether aggregation is present. Dispersion of the amide chemical shifts is an indicator of the former, whereas a narrow distribution, in the range of 7.5-8.5 ppm, is characteristic of unstructured peptides. Aggregation leads to broad peaks and spectra of poor quality. Adjustment of conditions by varying pH, buffer, cosolvent (e.g., acetonitrile for hydrophobic peptides), or peptide concentration and monitoring the effects on ID spectra is often used to find optimum conditions. 

Figure 12.9 displays graphically the proton chemical shifts of all 20 amino acids in an unstructured peptide context. These are called random coil chemical shifts because they are not influenced by the through-space effects observed in specifically folded proteins. In this environment, there is not much chemical-shift dispersion Hn falls between 8 and 9 ppm, Ha between 4 ppm and the water resonance ( 4.8 ppm), and the side-chain Hn resonances... 

Peptide bonds are planar and can be either in the trans or in the cis conformation with respect to the two successive C positions. These conformations are equivalent to dihedral angles trans state is strongly favored for peptide bonds that do not involve proline residues. The cis conformation has not been detected in unstructured, linear oligopeptides, and the equilibrium population of the cis form is believed to be less than 0.1% (Brandts et al., 1975, Jorgensen and Gao, 1988). Very few nonproline cis peptide bonds have been found in native, folded proteins by X-ray crystallography (Stewart et al, 1990 MacArthur and Thornton, 1991). 

Metallopeptide models refer to systems that are mostly unstructured in solntion in the absence of metal ions. It is applicable to design of metal-binding sites whose conserved residues appear mostly in a single peptide that is often much shorter than the whole protein. Designing metalloproteins using only the peptide with the consensus sequence, often called a motif, represents the minimalist approach in its purest sense. These motifs typically contain His, Cys, or both residues. In addition, metalloporphyrin-containing peptides have also been made to mimic basic features in heme proteins. 

To obtain secondary structure information of the cAPP peptides, CD spectra were recorded in different solvents. These data (not shown) provided strongly negative ellipticities around 200 nm in both phosphate buffer (pH 7) and deionised water, indicating flexible, unstructured states. 

In this review, we will discuss the aggregation of three intrinsically unstructured peptides and proteins and the diseases to which they contribute. Specifically we wiU concentrate on amyloid-P (A ), islet amyloid polypeptide (LAPP), and a-synuclein. 

In general, there is a simple picture of the events that occur during oligomerization of natively unstructured protein and peptides unfolded monomers undergo organized self-assembly via several intermediate assemblies on the pathway to fibrils. Many of these intermediates have been characterized and named based on in vitro studies, but there is no defined nomenclature as of yet. The following intermediates have been identified so far in the fibril polymerization process ... 

Far UV circular dichroism spectra contain information about secondary structure content in proteins and peptides. Small peptides are almost invariably unstructured in aqueous solution, but can adopt regular secondary structure upon binding to a protein. In general, the secondary structure of a protein is unlikely to change dramatically upon binding to a peptide. However, as shown in this work, the binding of a target peptide to a mutated protein with an altered structure (compared with the wildtype) may partially restore the "native" structure of the protein. 

Fig. (10). Representation of the functional determinants of fowIicidin-1. The C-terminal a-helix (Glyl6 - lie 23) is required for the three activities of the peptide antibacterial, cytolitic, and LPS-binding. The N-terminal unstructured region (VaI5-Pro7) comprises the second determinant that is importantly implicated in citotoxicity and LPS-binding. The a-helix (Leu8-AIal5) also most likely enables the interaction of the C-terminal helix with lipid membranes. Reprinted with permission from [148]. Copyright (2006) Blackwell Publishing.

---