Peptides coiled coils

A later paper details the de novo design of peptides that switch between a coiled-coil and a helical-hairpin conformation. The parent peptide (coiled-coil switch peptide) CSP-1 is a parallel dimeric coiled coil, but oxidation of cysteine residues in (he peptide causes the switch to a monomer. It remains ar-helical, although the a-helical content is low. Increasing the loop length gives CSP-3, which is a peptide with a higher helical content. CSP-6, an anagram of CSP-3, is more helical stUl and can be switched between the helical-hairpin and coiled-coil conformations. 

Keywords Artificial peptides Coiled-coil structure Helix structure ... 

Ghosh etal. also used CD spectroscopy to assess the association affinities of peptide coils in the absence and presence of bound Hg + or Cd +. These authors constmcted a family of peptides having secondary stmctures that bind metal ions in a trigonal thiolate coordination environment, even metal ions like Hg + and Cd + that prefer tetrahedral coordination geometries. Their results indicate increased stability of coUed-coU peptide structures upon addition and binding of the metal ions, and support the hypothesis that favorable tertiary interactions within the protein systems allow for stabilizing the non-preferred coordination geometry of the bound metal ions. 

Leitner DM. 2002. Anharmonic decay of vibrational states in helical peptides, coils and one-dimensional glasses. J. Phys. Chem. A 106 10870-10876. 

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). 

Nonrepetitive but well-defined structures of this type form many important features of enzyme active sites. In some cases, a particular arrangement of coil structure providing a specific type of functional site recurs in several functionally related proteins. The peptide loop that binds iron-sulfur clusters in both ferredoxin and high potential iron protein is one example. Another is the central loop portion of the E—F hand structure that binds a calcium ion in several calcium-binding proteins, including calmodulin, carp parvalbumin, troponin C, and the intestinal calcium-binding protein. This loop, shown in Figure 6.26, connects two short a-helices. The calcium ion nestles into the pocket formed by this structure. 

Formation of helical-like peptides stabilized due to heterocyclic bridges formed between coils by natural and artificial amino acids 99T11711. 

Weidner and Engel142 used the relatively short collagen peptide al-CB2 as a model peptide for kinetic measurements. They observed that the rate at the beginning of the helix formation, starting from purely coiled chains, obeys the following equation ... 

In 1% aqueous acetic acid, the peptides of the sequence (Ala-Gly-Pro)n, bridged with Lys-Lys and beginning with n = 8 show a cooperative transition, which was interpreted as a triple helix-coil transition (see Figs. 35, 36). 

Table 8. Thermodynamic parameters of the coil-to-helix transition of collagen-model peptides, covalently linked with 1,2,3-propanetricarboxylic acid (PTC) and Lys-Lys, respectively. Solvent 1% aqueous acetic arid (pH 3.0)...

Because of these observations, comparative experiments with peptides of different proline content in a solvent less polar than water, are recommended. (Pro-Pro-Gly)n and (Pro-Ala-Gly)n, in methanol/acetic add (volume ratio 9 1) show a temperature-induced triple helix-coil transition which is characterized by the following parameters92,150) (Pro-Pro-Gly)n AH°s = -1.9 kJ/rnol tripeptide AS° = -5.4 J tnor1 K (Pro-Ala-Gly) A HI = -0.9 kJ/mol tripeptide A 5° = -3.8 J mol-1 K ... 

Since 1973, several authors have proved that there is a relationship between thermostability of collagen and the extent of hydroxylation of the proline residues31,34). Equilibrium measurements of the peptides al-CB 2 of rat tail and rat skin revealed a higher rm, for al-CB 2 (rat skin)157). The sequence of both peptides is identical except that in the peptide obtained from rat skin, the hydroxylation of the proline residues in position 3 has occurred to a higher extent than in the case of al-CB 2 (rat tail). Thus, a mere difference of 1.8 hydroxy residues per chain causes a ATm of 26 K. Obviously, there are different stabilizing interactions in the triple-helical state, that means al-CB 2 (rat skin) forms more exothermic bonds than al-CB 2 (rat tail) in the coil triple-helix transition. This leads to an additional gain of enthalpy which overcompensates the meanwhile occurring losses of entropy. 

Many enveloped viruses share a common mechanism of fusion, mediated by a virus-encoded glycoprotein that contains heptad repeats in its extraceUnlar domain. Dnring the fnsion process, these domains rearrange to form highly structured and thermodynamically stable coiled-coils. Viruses encoding fusion proteins that have these domains inclnde members of the paramyxovirus family (e.g., respiratory syncytial virus, metapneumovirus, and measles virus), ebola virus, influenza, and members of the retroviridae (e.g., human T cell lenkemia virus type-1 and human immunodeficiency virus type-1, HlV-1). Peptide inhibitors of fusion that disrupt the... 

Fig. 3.17 Activation of gene transcription by artificial transcription factors. (Top) The artificial activator is composed of three separate functional domains. The DNA binding domain consists of the pyrrole/imidazole polyamides (shown as connected arrows). A tethered linker domain (shown as a coil) connects the DNA binding domain to the peptide activation domain (AD, shown as an oval).

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. 

Since our original aPNA publication, there have been other reports of the incorporation of nucleobases into a-helical peptides. Mihara and coworkers reported that a-hehcal coiled-coiled peptides could be stabilized by base pairs between complementary y-nucleobase-a-aminobutanoic acids [78] They have also reported that the incorporation of such nucleoamino acids into a-hehcal segments of HIV-1 Rev and HIV-1 nucleocapsid protein can result in increased binding affinity and specificity to HIV-1 RRE RNA and SL3 RNA respectively [79, 80]. 

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 ... 

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