Improved manual sequential analysis of peptides.

Organic solvents can affect the efficiency of peptide sequencing by the Edman degradation method by altering peptide extractive losses during manual sequence analysis. We present a modified phenylisothiocyanate procedure for the degradation of one to five peptides simultaneously with high repetitive yield (90–95%) with an average time per cycle of 75 min. Improvement in average yield per cycle (repetitive yield) varies with the choice of solvent and nature of peptide under investigation. The degree of extraction of a particular thiazolinone similarly can be improved by the selection of appropriate solvents.     

Purification of naturally occurring peptides by reversed-phase HPLC

Reversed-phase high performance liquid chromatography (HPLC) has become the method of choice for the purification of peptides and small proteins (M(r) < 10,000 Da) from natural sources. The technique combines high resolution and recovery with ease and speed of operation and is applicable to a wide range of peptides with different physicochemical properties. This protocol describes procedures for (1) the extraction of a biologically active peptide from animal tissue, (2) concentration of the extracts and partial purification on Sep-Pak cartridges, and (3) purification to near homogeneity on a range of silica-based HPLC columns. Standard operating procedures involve acetonitrile as organic modifier, trifluoroacetic acid as ion-pairing reagent and sequential chromatographies on octadecyl (C18), butyl (C4) and diphenyl wide-pore (300 A) columns under gradient elution conditions. The limiting factor in the time taken to isolate a peptide is usually the speed at which assays to detect the peptide can be performed, but purifications can generally be accomplished within 1 or 2 weeks.     

Recovery of biologically active enzymes after HPLC separation

The mass and activity recovery of eight different enzymes (two monomeric, six oligomeric) with molecular masses between 25,000 and 240,000 daltons were tested after HPLC separation on three different HPLC instruments (two with stainless steel and one with titanium flow paths). Most of the tested proteins are known to be sensitive to heavy metal ions. Eight wide pore, ion-exchange columns, two size-exclusion columns and two hydrophobic-interaction columns were used. Both stainless steel and glass column hardware were used in all three separation modes. The elution times were between 8 and 12 minutes. In almost all cases, the activity recovery was between 90% and 100% compared with a control sample incubated in the chromatographic elution buffer for the same time at the same temperature. A severe activity loss (about 30%) was observed with only one ion-exchange column and one enzyme. Neither the column hardware nor the material of the HPLC equipment had any negative effect on the activity recovery of the enzymes tested.     

The relevance of imidazole tautomerism for the hormonal activity of histidine-containing peptides

Substitution of 5-nitro- -histidine for -histidine is proposed as a useful tool to study the relationships among tautomerism, acid-base properties, and biological activity of peptide hormones. This approach is illustrated by an analog of the tripeptide thyroliberin, [5-nitro- -histidine]²-thyroliberin, which has been prepared by solid-phase peptide synthesis. The acid-base properties of the hormone analog and the position of the imidazole ring tautomeric equilibrium have been investigated by spectroscopic methods. Correlation of these properties with the biological activity of the nitrated tripeptide strongly supports the idea that imidazole ring tautomerism is a key factor for hormonal activity and that the N^τ-H tautomer must be considered the biologically active form of thyroliberin.     

Improved separation of sterols by column chromatography

Some closely related sterols have been separated on columns of neutral alumina-Super-Cel impregnated with silver nitrate. Most notable are the separations of some Delta(8)-sterols from their Delta(7)-isomers, separations which have been difficult, if not impossible, to achieve with other published column chromatographic methods.     

Optimum separation condition of peptides in reversed-phase liquid chromatography

An efficient optimization method was suggested to separate biologically active peptides by RP-HPLC. In this work, the binary mobile phase of water and acetonitrile was used with the buffer of trifluoroacetic acid (TFA). The elution profiles were calculated by the plate theory based on the linear and quadratic equations of retention factor, lnk=A+BF, lnk=A+BF+CF(2), and F was the vol.% of acetonitrile. We modified the plate theory to calculate elution profile in both isocratic and gradient mode. From the final calculated results, the first mobile phase composition was water in 0.1% TFA/acetonitrile in 0.1% TFA, 81/19vol.%, then after 7-8 min, the second composition of mobile phase was linearly changed to 79/21vol.%, and finally after 8 min, it was kept at the isocratic mode. In the experimental conditions, the agreement between the experimental data and the calculated values was relatively good.     

Improved antimicrobial peptides based on acyl-lysine oligomers

We describe peptidomimetic oligomers that show rapid, nonhemolytic, broad-spectrum bactericidal properties in mice and do not induce the emergence of resistance. The oligomers contain acyl chains, which prevent the formation of stable secondary structure. This design appears advantageous over conventional antimicrobial peptides with respect to in vivo efficacy and safety, and may provide a convenient platform for the development of peptide antibiotics.     

Improved prediction of signal peptides: SignalP 3.0

We describe improvements of the currently most popular method for prediction of classically secreted proteins, SignalP. SignalP consists of two different predictors based on neural network and hidden Markov model algorithms, where both components have been updated. Motivated by the idea that the cleavage site position and the amino acid composition of the signal peptide are correlated, new features have been included as input to the neural network. This addition, combined with a thorough error-correction of a new data set, have improved the performance of the predictor significantly over SignalP version 2. In version 3, correctness of the cleavage site predictions has increased notably for all three organism groups, eukaryotes, Gram-negative and Gram-positive bacteria. The accuracy of cleavage site prediction has increased in the range 6-17% over the previous version, whereas the signal peptide discrimination improvement is mainly due to the elimination of false-positive predictions, as well as the introduction of a new discrimination score for the neural network. The new method has been benchmarked against other available methods. Predictions can be made at the publicly available web server     

Improved automated solid-phase microsequencing of peptides using DABITC

The methylated purines O⁶-methyl- and 7-methylguanine were isolated from mouse liver DNA hydrolysates by means of a column cleanup employing a Sep Pak C-18 reverse-phase cartridge. The purine bases were eluted from the cartridge with methanol, evaporated to dryness, and then dissolved in mobile phase for liquid chromatographic analysis by normalphase chromatography. The system consisted of a LiChrosorb Si 60 column with a watersaturated mobile phase of 20% methanol in chloroform containing 0.001% H₃PO₄. The two methylated bases eluted before adenine or guanine. For extremely low-level (<300 pmol) quantitation, the peaks corresponding to O⁶-methyl- and 7-methylguanine were collected and then analyzed by reverse-phase chromotography with a LiChrosorb RP-18 column and a mobile phase of 5% methanol in pH 7 phosphate buffer (for 7-methylguanine) or 9.5% methanol/buffer (for O⁶-methylguanine). Comparisons were made with fluorescence detection and with scintillation counting (in animal studies where [¹⁴C]dimethylnitrosamine was used). Minimum detectable levels at 254 nm were about 3 ng (3:1 signal to noise ratio) for each of the title compounds. As low as 10 pmol/mg of each could be detected in DNA hydrolysates. Recoveries of O⁶-methyl- and 7-methylguanine from DNA spiked at 750 pmol/mg were greater than 80%.     

HPLC separation and indirect ultraviolet detection of phosphorylated sugars

An HPLC method for the separation and analysis of phosphorylated sugars is presented. Ion-exchange chromatography coupled to indirect ultraviolet detection has produced good resolution and sensitivity. Fructose 6-P, glucose 6-P, ribose 5-P, 3-phosphoglyceric acid, ribulose 1,5-P₂, fructose 1,6-P₂, and sedoheptulose 1,7-P₂ can be separated at a sensitivity down to 10 nanomoles. The system resolves 2-carboxy-D-arabinitol 1,5-P₂ from 2-carboxy-D-ribitol 1,5-P₂. The natural inhibitor of ribulose bisphosphate carboxylase, 2-carboxy-D-arabinitol 1-P, has been separated from its 5-P isomer and most other phosphorylated compounds. This method is applied to identification of the products obtained upon ion-exchange purification of synthetic 2-carboxyarabinitol 1-P.     

Improved methods for separation of human cytokeratins.

The cytokeratins from human bladder and esophageal epithelia were separated using chromatographic techniques. The cytokeratins were first extracted from fresh autopsy tissue using high and low salt buffers. Urea, 8.0-9.5 M, was used to solubilize the resulting cytokeratin pellet. Imidazole was found to increase the solubility of the pellet but reducing agents such as 2-mercaptoethanol were not beneficial. DEAE ion exchange chromatography produced three fractions which were analyzed by using one and two-dimensional electrophoresis. The third fraction was shown to contain the acidic cytokeratins and was further fractionated on a moderately polar reverse phase HPLC column using an acetonitrile elution gradient. Tetramethylammonium tetrafluoroborate was added to the mobile phase to react with any unreacted silanol groups on the stationary phase, and trifluoroacetic acid was added to ion pair with the protein. HPLC fractions of the acidic proteins from human esophagus revealed seven reproducible peaks. All seven peaks were shown by Western blotting to contain an epitope found on cytokeratin 13. The results suggest that the isolation and separation procedures have produced a series of peptide products which all retain a similar epitope but which vary significantly in their hydrophobic characteristics.     

High-performance immobilized metal ion affinity chromatography of peptides: analytical separation of biologically active synthetic peptides

The separation of more than 30 biologically active synthetic peptides and their analogs on a high-performance immobilized metal ion affinity chromatography column is described. The metal chelating gel (TSK gel chelate-5PW) contains iminodiacetic acid (IDA) covalently coupled to a hydrophilic, resin-based matrix with a bead diameter of 10 micron. The retention of the peptides on Cu(II), Ni(II), and Zn(II) ions immobilized on the chelating gel showed that some of them can be separated by isocratic elution while the majority of them are retained and are separated into distinct fractions by elution with a linear imidazole gradient or with a continuously decreasing pH gradient. Of the three immobilized metal ions investigated here, the IDA-Cu(II) chelate column gave the best resolution irrespective of the type of gradient used. This is amply illustrated by the resolution of angiotensins I and II and their seven synthetic analogs. The results obtained here serve as guidelines for the future exploitation of this separation method for the efficient fractionation of a wide variety of peptides on an analytical or preparative scale.     

Improved separation of sterols by reversed-phase thin-layer chromatography

Some closely related sterols have been separated with better resolution in a shorter period of time than has previously been reported. Separations were effected on the basis of carbon number and the number and location of double bonds through the use of paraffin-impregnated kieselguhr chromatoplates in the system (paraffin oil)/(acetone-water 4:1).