In the Laboratory

268 Journal of Chemical Education • Vol. 77 No. 2 February 2000 • JChemEd.chem.wisc.edu

Dipeptide Sequence Determination: Analyzing WPhenylthiohydantoin Amino Acids by HPLCJanice S. Barton,* Chung-Fei Tang, and Steven S. ReedDepartment of Chemistry, Washburn University, Topeka, KS 66621; *zzbart@washburn.edu

Rationale

Amino acid composition and sequence determinationrepresent important biochemical techniques for characterizingpeptides and proteins. Prediction of protein secondary andtertiary structure (1–3) relies on accurate sequence information.Database comparisons for sequence alignment reveal sequencehomologies and are instrumental in establishing evolutionaryand functional relationships and for identifying motifs orsupersecondary structure (1–3). Although automated Edmandegradation and DNA sequence determination are prominenttechniques for establishing the sequence of proteins, manualmethods can enhance students’ understanding of the prin-ciples and techniques of sequence analysis. Thus, biochemicallaboratory textbooks often include experiments for determi-nation of the composition (4 ), N-terminal residue (5), orsequence of a dipeptide (6–8). Historically, these textbookexperiments employed combinations of paper and thin-layerchromatography detection procedures, which have limitedresolution. A composition determination procedure thatinvolves separating fluorenylmethyl chloroformate derivativesby HPLC (9) and an amino terminal analysis of PTH (phenyl-thiohydantoin) amino acids by HPLC (7 ) adapt newertechnologies to instructional laboratories. PTC (phenylthio-carbamyl) derivatives of amino acids can be used to definethe composition of amino acid mixtures, and their resolutionby HPLC (10, 11) drastically reduces the time requiredfor amino acid analysis. Apparently, however, these PTCmethods have not yet been incorporated into the laboratorycurriculum.

Most PTC-amino acids are negatively charged owing tothe free α-carboxyl group; basic amino acids are the possibleexception. In contrast, any charge on the PTH–amino acidwould arise from the side chain. Consequently, the experi-mental conditions for separation of PTC– and PTH–aminoacids by HPLC differ. Use of two HPLC protocols to deter-mine the sequence of a dipeptide poses a logistics problem foruse in biochemistry instructional laboratories. Instead, it isdesirable to have one HPLC protocol for both compositionand sequence analysis. Since PTC derivatives are convertedinto the PTH form during the Edman degradation to identifythe N-terminal amino acid, it seemed prudent to employPTH derivatives for composition determination as well.

The experimental techniques presented in this commu-nication use PTH derivatives and HPLC to determine both thecomposition and sequence of dipeptides. The method can alsobe used solely for amino terminal analysis. From this instruc-tional procedure, students learn some principles and practicalapplication of HPLC as well as a major synthetic methodfor peptide and protein analysis. The protocol for formationof PTH derivatives is simplified and replaces aqueous pyridinewith ethanol and triethylamine. In this conversion process,the more common concentrated hydrochloric acid (HCl) is

substituted for trifluoroacetic acid (TFA). Serine and threoninemay serve as components of the unknown dipeptide whenconcentrated HCl replaces the dehydrating TFA. Formationof PTH derivatives in both the N-terminal and compositionsteps of sequence determination allows use of a single solventsystem for reverse phase HPLC analysis.

Methods

This experiment involves N-terminal analysis by theEdman method and hydrolysis of a dipeptide with subsequentdetermination of dipeptide composition with a modifiedEdman procedure. Determination of the N-terminal residueusing the Edman degradation procedure may be characterizedby the steps of coupling, washing, cleavage, extraction, andconversion (12, 13). Subsequent to hydrolysis, peptidecomposition determination requires coupling, washing, andconversion. Student pairs can accomplish both procedures(synthesis of the N-terminal and hydrolyzed dipeptide PTHderivatives) in one 3-hour period. This time compaction isbest achieved if each partner performs one of the two tasks,N-terminal or composition analyses, and the students havepreviously performed hydrolysis of the dipeptide used forcomposition analysis.

The PTH–amino acids are analyzed by reverse phaseHPLC on a C18 column with a one-step gradient elutionprocedure of 20-minute duration. Inexpensive columns aresufficient for simultaneous resolution of derivatives of aspartate,serine, glycine, alanine, proline (or valine), leucine, and phenyl-alanine (or lysine) using a single-step gradient elution process.Isocratic methods, with which we have no experience, areavailable (14 ). This procedure is similar to other HPLC pro-tocols for PTC– and PTH–amino acids in that it requiresmaintenance of the column temperature near 50 °C. Thetemperature is maintained by an immersion circulator withthermostat that pumps heated water through a column jacket.The column jacket is a simple, inexpensive device (insulatedcopper tubing wound to fit around the column) that workswell, giving good retention time precision.

Results

Dipeptide samples for students were selected for a com-bination of readily resolvable PTH–amino acids. These dipep-tide combinations were composed of amino acids with sidechains (aliphatic, acidic, basic, polar uncharged, and aromatic)of differing polarity. For chromatographic analysis, studentswere given the individual known PTH–amino acids and wereexpected to obtain a chromatogram for each known, theiramino-terminal derivative, and the mixture of PTH derivativesgenerated from the hydrolyzed dipeptide. Identification ofthe N-terminal amino acid and the composition of thedipeptide were made from observed retention times. Table 1

In the Laboratory

JChemEd.chem.wisc.edu • Vol. 77 No. 2 February 2000 • Journal of Chemical Education 269

contains retention times for acomplex mixture of PTH–amino acids separated on anAlltech Absorbosphere C18HPLC column. The value ofstandard deviations for tripli-cate retention times is ±0.07minutes or less.

As described here, theHPLC experiment requiresone laboratory period for eachpartnership. The time require-ment can be reduced by giv-ing the students the mixtureof known PTH–amino acidsand identification of the elu-tion order. Each partnershipcan then obtain chromato-grams for the standard mix-

ture, the N-terminal derivative, and the hydrolyzed dipep-tide in about an hour. Two to three groups can operate theHPLC in a 3- to 4-hour period. For laboratory sessions withlarge enrollments, the number of students in a group can beincreased or use of the HPLC can be scheduled outside of theclass period.

This experiment, developed over a period of three to fiveyears, has been highly successful. Dipeptide combinations ofamino acids differing in retention times by about 1 minutewere successfully identified by students enrolled in an upper-division biochemistry laboratory course with a prerequisiteof one semester of organic chemistry laboratory.

Chemicals and Equipment Needed

Phenylisothiocyanate suitable for protein sequencing wasobtained from Aldrich. Dipeptides and PTH–amino acidswere obtained from Sigma. The acetonitrile should be HPLCgrade. Nylon 66 filters with 0.45-µm pore size should be usedto filter samples (4-mm diam) and solvents (45-mm diam).A rotatory evaporator and a variable micropipet (100–1000µL) are very useful performance-enhancing items. The HPLC,equipped with a UV detector set at 254 nm, must have twopumps and the ability to deliver a solvent gradient eitherinternally or by computer. An inexpensive C18 Econosphere

5-µm particle column (250 × 4.6 mm) may be purchasedfrom Alltech. An immersion circulator with thermostat anda column water jacket are required for HPLC.

Acknowledgments

Partial support for this work has been provided by theNational Science Foundation’s College Science Instrumen-tation Program, grant #CSI-855 8650399, and a researchgrant from Washburn University.

WSupplemental Material

The complete description of this experiment and supple-mental material are available in this issue of JCE Online.

Literature Cited

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ology in Biochemistry: Amino Acid Analysis and Protein Sequenc-ing, Fini, C.; Floridi, A.; Finelli, V. N.; Wittman-Liebold, B.,Eds.; CRC Press: Boca Raton, FL, 1990; pp 109–128.

4. Crandall, G. D. Biochemistry Laboratory; Oxford UniversityPress: New York, 1983.

5. Rendina, G. Experimental Methods in Modern Biochemistry; Saun-ders: Philadelphia, PA, 1971.

6. Clark, J. M. Jr.; Switzer, R. L. Experimental Biochemistry, 2nded.; Freeman: New York, 1977.

7. Boyer, R. F. Modern Experimental Biochemistry, 2nd ed.; Ben-jamin/Cummings: Redwood City, CA, 1993.

8. Rogers, P. W. J. Chem. Educ. 1996, 73, 189.9. Clapp, C. H.; Swan, J. S. J. Chem. Educ. 1992, 69, A122–

A126.10. Bidlingmeyer, B. A.; Cohen, S. A.; Tarvin, T. L. J. Chromatogr.

1984, 336, 93–104.11. Ebert, R. F. Anal. Biochem. 1986, 154, 431–435.12. Schroeder, W. A. Methods Enzymol. 1967, 11, 445–461.13. Robyt, J. F.; White, B. J. Biochemical Techniques, Theory and

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rofsemiTnoitneteR.1elbaTsdicAonimA–HTP

dicAonimA–HTP nim/emiTeninalA 67.5

etatrapsA 14.2enicylG 83.4enicueL 92.21(enisyL ε )CTP- 78.11

enicuelroN 26.21eninalalynehP 36.11

enilorP 98.9enireS 06.3enilaV 86.9

Note: An Absorbosphere C18,250 × 4.6-mm column was used.Norleucine may be used as aninternal standard.