Temperature and peptides

Figure 2 The change in fraction folded of a coiled-coil leucine zipper peptide, GCN4-P1, as a function of temperature and peptide concentration. The concentrations range from 1 pM with the lowest Tu to 20 pM with the highest T. The enthalpy of unfolding was 35.0 1.1 koal moM (monomer) which compared to that of 34.7 0.3 koal moM measured by calorimetry. Abstracted with permission from data in Thompson KS, Vinson CR and Freire E (1993) Biochemistry Z2 5491-5496. Copyright 1993 American Chemical Society.

The FAB source operates near room temperature, and ions of the substance of interest are lifted out from the matrix by a momentum-transfer process that deposits little excess of vibrational and rotational energy in the resulting quasi-molecular ion. Thus, a further advantage of FAB/LSIMS over many other methods of ionization lies in its gentle or mild treatment of thermally labile substances such as peptides, proteins, nucleosides, sugars, and so on, which can be ionized without degrading their. structures. 

Figure 3.13 shows the thermal stability of immobilized ODN and PNA. The signal for the Thy- and Cyt-bases obtained with temperature-programmed (TP) SIMS starts to decrease at approximately 150 °C for ODN and 200 °C for PNA. This variance is caused by the different strengths of binding between the bases and the sugar-phosphate and peptide backbones, respectively. 

Protected 3-methyl-D-cystein (257 Scheme 3.94), a structural unit of the peptide antibiotics nisin and subtilin, has been synthesized through the ring-opening of the aziridinecarbamide 254 with thiobenzoic acid (255) [143, 144]. The reaction took place overnight at room temperature and in methylene chloride to give 256 in greater than 95% yield. 

A simple predecessor of the CEM setup for microwave-mediated SPOS was employed by Murray and Gellman in their synthesis of 14-hehcal 6-peptides [42], A 4 mL polypropylene solid-phase extraction tube was inserted into a 10 mL CEM vessel, allowing for both microwave heating and simple resin manipulation (Eig. 11). While using this setup gave reproducible results for their experiments, a discrepancy between the reactions target (set) temperatures and the actual temperatures was observed. Therefore, use... 

Once the resolution has been optimized as a function of gradient rate, one can continue to fine-tune the separation, raising flow rate and temperature. In a study of temperature and flowrate variation on the separation of the tryptic peptides from rabbit cytochrome c, column performance doubled while analysis time was reduced by almost half using this strategy.97 Commercially available software has been developed to aid in optimization. As a final note, in an industrial laboratory optimization is not completed until a separation has been shown to be rugged. It is a common experience to optimize a separation on one column, only to find that separation fails on a second column of identical type. Reproducibility and rigorous quality control in column manufacture remains a goal to be attained. 

A high-speed separation of tryptic peptides of horse cytochrome c is shown in Figure 6. As the temperature and flow rate were increased, the separation substantially improved, an observation consistent with data demonstrating that conformational issues may be increasingly important factors in peak broadening as the time scale of the chromatography approaches that... 

Figure 6 High-speed tryptic fingerprint. Horse cytochrome c was digested with trypsin and the peptide chromatographed in acetonitrile water 0.1% TFA at various temperatures and flow rates on a 15 x 0.2-cm PS-DVB column packed with 3-p, 300-A particles, (a) 26°C and 0.5 ml/min. (b) 42°C and 0.7 ml/min. (c) 70°C and 1.1 ml/min. Detection at 220 nm. Note that the resolution rises with the speed of separation.89 (From Swadesh, ]., BioTechniques, 9, 626, 1990. With permission.)...

The processes of both seed formation and fibril extension are dependent on temperature and on peptide concentration, with 37°C being required for establishing equilibrium within 24 h with 30 pM Pi 4o- A full description of the assay system may be found elsewhere [97,117], A 4 h reaction time is typically within the linear portion of the time course. This nucleus-dependent assay detects mainly inhibitors that are substoichiometric with the monomeric peptide, which is present at high concentration. It is relatively insensitive to inhibitors that target the monomeric peptide. Whether the inhibitors interact with the growing end of a seed or with a low abundance conformational form of the p peptide that is competent to add to the seed is difficult to determine at this time. Similar dose-response curves are obtained for Congo Red as an inhibitor with either thioflavin T (ThT) fluorescence or filtration of radioiodinated peptide readouts (Fig. 4) Caveats in the interpretation of both the ThT and radiometric filtration assays for the evaluation of putative inhibitors are discussed elsewhere [97]. 

The broad use of A -carbonyldiimidazole (CDI) for the synthesis of amide and peptide linkages became a routine method only in the early sixties. JV-Protected amino acids were treated at room temperature with an equimolar amount of CDI to give imidazolides. Anhydrous tetrahydrofuran, dimethoxyethane, dichloromethane, pyridine, dimethylfor-mamide, and diethyl phosphite were utilized as solvents. In the second step the esters of amino acids, their hydrochlorides, or sodium salts were added to yield the peptide after several minutes or hours of reaction time. 

Selective cleavage of peptides and proteins is an important procedure in biochemistry and molecular biology. The half-life for the uncatalyzed hydrolysis of amide bonds is 350 500 years at room temperature and pH 4 8. Clearly, efficient methods of cleavage are needed. Despite their great catalytic power and selectivity to sequence, proteinases have some disadvantages. Peptides 420,423,424,426 an(j proteins428 429 can be hydrolytically cleaved near histidine and methionine residues with several palladium(II) aqua complexes, often with catalytic turnover. 

The presence of a solvent, especially water, and/or other additives or impurities, often in nonstoichiometric proportions, may modify the physical properties of a solid, often through impurity defects, through changes in crystal habit (shape) or by lowering the glass transition temperature of an amorphous solid. The effects of water on the solid-state stability of proteins and peptides and the removal of water by lyophilization to produce materials of certain crystallinity are of great practical importance although still imperfectly understood. 

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