Peptide in water

Elber et al. [48] applied this method to explore the dynamics of the C-peptide in water with impressive results. More than 30 trajectories of C-peptide were generated, and the process of helix fonnation in water was examined. Remarkably, a time step of 500 ps was used, which allowed for the study of peptide folding on extended time scales. 

Experimental and theoretical approaches are now converging on the polyproline II backbone conformation as the most stable structure for short alanine peptides in water. It becomes of urgent importance to determine the energy differences between polyproline II and other possible backbone conformations, as well as to determine how amino acid composition and sequence affect backbone conformation. 

In balance, the small decrease in enthalpy (AH < 0) is more than offset by a large decrease in entropy (AS < 0) so that the overall reaction is unfavorable. Thus, one would not expect to see the formation of single hydrogen bonds between two peptides in water. This is what is found. 

Tirado-Rives ). and Jorgensen W. L. Molecular dynamics simulations of the unfolding of an alpha-helical analogue of ribonuclcase A S-peptide in water. Biochemistry (1991) 30(16) 3864-71. 

As the solubility of this peptide in water is very low, the peptide can be associated with the liposomal membrane. As the peptide is only sparingly soluble in methanol or chloroform, DMSO had to be used as dissolution medium for mixing the peptide with the lipids for liposome formation. A lOmg/mL stock solution in DMSO of the peptide could be obtained. Appropriate amounts of lipid stock solutions and the peptide stock solution were mixed (lipid peptide ratio = 95 5) and processed as thoroughly described in the... 

Tomeiro M, Still WC. Sequence-selective binding of peptides in water by a synthetic receptor molecule. J Am Chem Soc 1995 117 5887-5888. 

Monte Carlo and molecular dynamics calculations predict that, in aqueous solutions, the a-helix is substantially more stable than the 310-helix for (Ala), 79 and even for a decamer of Aib. 80 Thus, it seems very unlikely that Ala-rich peptides in water have any significant level of molecules that are wholly or largely in the 310-helix. However, isolated 310-helix hydrogen bonds or perhaps short stretches of 310-helix near the termini are possible. High-resolution NMR of the peptides Ac-(A4K)A-NH2 and Ac-AMAAKAWAAKAAAARA-NH2 81 have led to estimates of about 50% 3i0-helix population at the termini and 25% in the interior. The CD spectrum for a mixed a-310-helix has not been determined. 

Waks, M. (1986) Proteins and peptides in water-restricted environments. Proteins, 1,4-15. 

Hopkins and co-workers [6] have used the selective complexation of transition metals by two distant EDTA modified amino acids to stabilize the a-helical conformation of peptides 2 and 3 (Fig. 3). The results were particularly impressive in the case of 3 where the helicity increased from 0 to about 80% upon complexation of Cd2 4 ions. Along the same lines, Ghadiri and coworkers [7] reported the important stabilization of the helical conformation of 4 and 5 by the formation of selective metal complexes (Ru2+, Zn2+, Cu2+, and Cd2+) involving either two imidazoles of histidines or one imidazole and one thiol from a cysteine separated by three amino acids (I, 1 + 4) (Fig. 4). They also reported that peptide 4 is Cd2+-selective and that the helical conformation of the inert Ru2+ complex of 5 is remarkably stable. For instance, it has a melting point 25 °C higher than the uncomplexed peptide in water. 

We will demonstrate in this chapter our approach towards modular receptors for complexation of biologically relevant peptides in water. A new binding motif for carboxylates, the guanidiniocarbonyl pyrroles, has been designed this enables the formation of stable ion pairs even in aqueous solvents. By a stepwise elongation of this binding motif with additional interaction sites receptors are obtained that bind not only carboxylates but also single amino acids, both side-chain- and ste-reoselectively, and even tetrapeptides. 

While empirical rules would fail to yield a correct conformational interpretation of the amide I spectrum, normal mode calculations using the SQM method clearly eliminate several possibilities and put forward a preferred structure for this peptide in water [70S], This approach can be extended to much larger peptides having stable secondary structures. We have collected spectra of several isotopomers of the 23-residue peptide magainin F. We observe in the difference spectra that the amide I bands corresponding to specific amino acids are much narrower than they are in the short peptides and clearly identify the amide I frequencies of these groups. 

By introducing a crown ether unit at the C-terminal region of hydrophobic helical peptides, Otoda et al.19 were able to demonstrate increased stabilization of the peptide aggregate in the membrane by the formation of sandwich-type complexes with large cations. Ion channel activity was also increased due to the ability of the crown peptide to bind ions to the terminal portion of the hydrophobic helix bundle at the water-lipid interface. Ueda et al.20 considered the problem of insolubility of hydrophobic peptides which restricts the distribution of peptides in water to a phospholipid bilayer membrane. In consequence they constructed a hydrophobic helix bundle shielded by hydrophilic peptides that acts rather like an umbrella. 

Straatsma and McCammon computed the PMFs for rotation around (j) and y of the alanine dipeptide in water, and then used these PMFs as a biasing potential to rapidly fold alanine tri- and hepta-peptides in water [89]. 

The immobilization of anti-P-endorphin to the carboxymethylated dextran (which is on the surface of the resonant layer) was via NHS/EDC chemistry. Prior to antibody coupling, the carboxymethylated dextran was activated twice with 0.4 M EDC/0.1 M NHS for 10 min. Anti-P-endorphin was coupled twice to the dextran layer in 10 mM sodium acetate buffer, pH = 5.0, at 25 pg/ml to ensure maximum loading. After coupling, the free activated carboxyl group was blocked with 200 pi of 1 M ethanolamine for two minutes. Finally, the cuvette with immobilized anti-p-endorphin was washed twice with 20 mM HCl and twice with PBS/0.05% tween 20, to eliminate the non-covalently bound antibody. The binding of the peptides to the antibody was carried out in PBS, pH=7.4, at 25°C. After the baseline was established for 150 pi of PBS, 50 pi of 3 mg/ml (0.1 mg/ml/peptide) crude peptides in water was added to the cuvette and the binding was monitored. When equilibrium was achieved (approximately 10 min), the unbound peptides were flushed away. 

Figure 5.31 Fibrous assembly of a planar cyc o-peptide in water. ...

Kritzer JA, Tirado-Rives J, Hart SA et al (2005) Relationship between side chain structure and 14-helix stability of p3-peptides in water. J Am Chem Soc 127 167-178... 

Fig. 8-3 Molecular imprinting of peptides in water by the use of metal complexation...

Reading of information in peptides relies on interactions between different side chains. It is hampered by the lack of conformational order, so that only a few peptide-recognition processes of peptides in water have beeen found (Peczuh et... 

Figure 2. Circular dichroic spectra for the X-D and X-O peptides, (a) CD scans reported at 5 °C in water, (b) Thermal unfolding scans of peptides in water.

Meara, J.P., Cao, B., Urban, J., Nakanishi, H., Yeung, E. and Kahn, M. (1994) Design and synthesis of small molecule initiators of a-helix structure in short peptides in water. In Maia, L.S. (ed.). Proceedings of the 23rd European Peptide Symposium, pp. 692-693. ESCOM, Leiden. 

HOC-Amino acids and peptides. The reagent reacts with sodium salts of amino acids (or peptides) in water to form the BOC derivatives in high yield. 

J01 Johansson, H.-O., Karlstrom, G., and Tjemeld, F., Temperature-indueed phase partitioning of peptides in water solutions of ethylene oxide and propylene oxide random eopolymers, Biophys. Acta, 1335, 315, 1997. 

A synthetic receptor, which is bound via non-covalent interactions to a dye, is able to function as a chemosensor. The basic requirement is that the displacement of the dye by an analyte results in a change of its optical properties. " Recently, it was shown that the combination of an organometallic Gp Rh complex with the dye azophloxine allows to selectively detect histidine- and methionine-containing peptides in water at neutral Due to the high... 

Next, we briefly summarize the result of applying our approach, in which the RISM theory is combined with the MC simulated annealing, to C-peptide in water. The initial conformation is an almost fully extended one (details of this conformation are described in 2.3). In the initial... 

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