Solvent peptides

Reaction of Co111 amine complexes with glycine esters gives products which are dependent on the solvent used (Scheme 7). In non-aqueous solvents peptide bond formation is observed.78"80 It is concluded that the reaction proceeds via the initial formation of a bidentate glycine ester complex in which the coordinated carbonyl group is activated (by the metal ion) towards nucleophilic attack by a further molecule of the glycine ester. Similar reactions have been observed with other Co111 complexes. 

Capasso S, Mazarella L, Zagari A. Deamidation via cyclic imide of asparagi-nyl peptides dependence on salts, buffers, and organic solvents. Peptide Res 1991 4(4) 234-238. 

Fig. 10. Highly schematic representation of the orientation of several tryptophan-containing peptides with respect to calmodulin. (A) With tryptophan in position 1, the indole is located on the hydrophilic side of the helix and is exposed to solvent. Peptides with tryptophan on this face of the helix should exhibit emission maxima near that of indole in water ( 350 nm), a small anisotropy, and a high accessibility for acrylamide quenching. (B) In position 2, the tryptophan is partially exposed at the interface between the peptide and calmodulin. Peptides with a tryptophan in this location should have fluorescence properties that are intermediate between example A and C. (C) The tryptophan is on the hydrophobic side of the helix and is almost entirely buried. The emission maximum should be strongly blue-shifted, the anisotropy should be large, and the accessibility to acrylamide quenching low. Taken from O Neil et al. (1987).

B. Feibush and E. GU-Av, Interaction between asymmetric solutes and solvents. Peptide derivatives as stationary phases in gas liquid partition chromatography. Tetrahedron 26 (1970), 1361. 

The hundreds of parameters qi,Ay,Bij, Cij,Dij, Ui, and / form a force field Additional sophisticated model parameter sets must be imposed, if the interaction of the protein with solvent molecules, ions, and counterions shall explicitly be considered For simulations in implicit solvent, peptide models can simply be extended by a solvation-energy... 

Caution During a sininlation, solvent temperature may increase wh ile th e so In te cools. This is particii larly true of sm all solven t molecules, such as water, that can acquire high translational and rotational energies. In contrast, a macromolecule, such as a peptide, retains most of its kinetic energy in vibrational modes. This problem rem ains un solved, an d this n ote of cau tion is provided to advise you to give special care to simulations using solvent. 

The biologiccJ function of a protein or peptide is often intimately dependent upon the conformation(s) that the molecule can adopt. In contrast to most synthetic polymers where the individual molecules can adopt very different conformations, a protein usually exists in a single native state. These native states are found rmder conditions typically found in Uving cells (aqueous solvents near neutred pH at 20-40°C). Proteins can be unfolded (or denatured) using high-temperature, acidic or basic pH or certain non-aqueous solvents. However, this unfolding is often reversible cind so proteins can be folded back to their native structure in the laboratory. 

With the dicyclohexylcarbodiimide (DCQ reagent racemization is more pronounced in polar solvents such as DMF than in CHjCl2, for example. An efficient method for reduction of racemization in coupling with DCC is to use additives such as N-hydroxysuccinimide or l-hydroxybenzotriazole. A possible explanation for this effect of nucleophilic additives is that they compete with the amino component for the acyl group to form active esters, which in turn reaa without racemization. There are some other condensation agents (e.g. 2-ethyl-7-hydroxybenz[d]isoxazolium and l-ethoxycarbonyl-2-ethoxy-l,2-dihydroquinoline) that have been found not to lead to significant racemization. They have, however, not been widely tested in peptide synthesis. 

To illustrate the specific operations involved, the scheme below shows the first steps and the final detachment reaction of a peptide synthesis starting from the carboxyl terminal. N-Boc-glycine is attached to chloromethylated styrene-divinylbenzene copolymer resin. This polymer swells in organic solvents but is completely insoluble. ) Treatment with HCl in acetic acid removes the fert-butoxycarbonyl (Boc) group as isobutene and carbon dioxide. The resulting amine hydrochloride is neutralized with triethylamine in DMF. 

Step 2 On reaction with hydrogen chloride m an anhydrous solvent the thiocarbonyl sulfur of the PTC derivative attacks the carbonyl carbon of the N terminal ammo acid The N terminal ammo acid is cleaved as a thiazolone derivative from the remainder of the peptide... 

The p nitrophenol formed as a byproduct in this reaction is easily removed by extrac tion with dilute aqueous base Unlike free ammo acids and peptides protected peptides are not zwitteriomc and are more soluble m organic solvents than m water... 

Critical micelle concentration (Section 19 5) Concentration above which substances such as salts of fatty acids aggre gate to form micelles in aqueous solution Crown ether (Section 16 4) A cyclic polyether that via lon-dipole attractive forces forms stable complexes with metal 10ns Such complexes along with their accompany mg anion are soluble in nonpolar solvents C terminus (Section 27 7) The amino acid at the end of a pep tide or protein chain that has its carboxyl group intact—that IS in which the carboxyl group is not part of a peptide bond Cumulated diene (Section 10 5) Diene of the type C=C=C in which a single carbon atom participates in double bonds with two others... 

For nonvolatile or thermally labile samples, a solution of the substance to be examined is applied to the emitter electrode by means of a microsyringe outside the ion source. After evaporation of the solvent, the emitter is put into the ion source and the ionizing voltage is applied. By this means, thermally labile substances, such as peptides, sugars, nucleosides, and so on, can be examined easily and provide excellent molecular mass information. Although still FI, this last ionization is referred to specifically as field desorption (FD). A comparison of FI and FD spectra of D-glucose is shown in Figure 5.6. 

Although simple solutions can be examined by these electrospray techniques, often for a single substance dissolved in a solvent, straightforward evaporation of the solvent outside the mass spectrometer with separate insertion of the sample is sufficient. This situation is not true for all substances. Peptides, proteins, nucleotides, sugars, carbohydrates, mass organometallics, and many... 

For mixture.s the picture is different. Unless the mixture is to be examined by MS/MS methods, usually it will be necessary to separate it into its individual components. This separation is most often done by gas or liquid chromatography. In the latter, small quantities of emerging mixture components dissolved in elution solvent would be laborious to deal with if each component had to be first isolated by evaporation of solvent before its introduction into the mass spectrometer. In such circumstances, the direct introduction, removal of solvent, and ionization provided by electrospray is a boon and puts LC/MS on a level with GC/MS for mixture analysis. Further, GC is normally concerned with volatile, relatively low-molecular-weight compounds and is of little or no use for the many polar, water soluble, high-molecular-mass substances such as the peptides, proteins, carbohydrates, nucleotides, and similar substances found in biological systems. LC/MS with an electrospray interface is frequently used in biochemical research and medical analysis. 

Soybean concentrate production involves the removal of soluble carbohydrates, peptides, phytates, ash, and substances contributing undesirable flavors from defatted flakes after solvent extraction of the oil. Typical concentrate production processes include moist heat treatment to insolubilize proteins, followed by aqueous extraction of soluble constituents aqueous alcohol extraction and dilute aqueous acid extraction at pH 4.5. 

Tables 1 and 2 Hst the important physical properties of formamide. Form amide is more highly hydrogen bonded than water at temperatures below 80°C but the degree of molecular association decreases rapidly with increa sing temperature. Because of its high dielectric constant, formamide is an excellent ionizing solvent for many inorganic salts and also for peptides, proteias (eg, keratin), polysaccharides (eg, cellulose [9004-34-6] starch [9005-25-8]) and resias.

---