A microcomputer program to calculate elemental analysis of peptides

A microcomputer program to calculate elemental analysis of peptides

Computer Methods and Programs in Biomedicine, 28 (1989) 119-120 119 Elsevier CPB 00959 Section II. Systems and programs A microcomputer program to ...

102KB Sizes 0 Downloads 1 Views

Computer Methods and Programs in Biomedicine, 28 (1989) 119-120


Elsevier CPB 00959 Section II. Systems and programs

A microcomputer program to calculate elemental analysis of peptides Stefano Mammi Centro di Studio sui Biopolimeri del Consiglio Nazionale delle Ricerche, Padua, Italy

A BASIC program is presented that calculates the elemental analysis of peptides given their primary sequence. This program is aimed to help synthetic chemists in the characterization of their products. The program runs on any IBM-compatiblecomputer with the MS-DOS operating system,version2.0 or greater, and the results are printable on any connected printer. Peptide synthesis; Elemental analysis; MS-DOS; BASIC

The chemical synthesis of peptides plays an important role in the understanding of a wide variety of biological events [1]. One of the tools most widely employed in the characterization of the adducts obtained is the quantitative analysis of the elements present in the compound [2]. The calculation of the theoretical percentage of each element in a peptide becomes increasingly long and tedious as the molecular weight of the comp o u n d increases, and errors can be introduced. A program is presented here which allows the synthetic chemist to simply introduce the desired sequence and to obtain results quickly and errorfree. The program, written in BASIC within the MS-DOS framework, accepts the peptide sequence as input, separates each group and searches for it in the library. The n u m b e r of times each element is present is summed over the entire sequence and the molecular weight is calculated as well as the weight percentage of each element. The calculation is limited to the most common elements

Correspondence: Stefano Mammi, Centro di Studio sui Biopolimeri del C.N.R., Via Marzolo 1, 35131 Padua, Italy.

present in peptides, i.e., C, H, N, O, S, F, CI, and Br. It is possible to add new groups to the library which is divided into three categories: amino acids with 50 possible entries, protecting groups with 220 possible entries, and crystallization salts with 30 possible entries. It is also possible to correct any mistake that might be present in the library, or view a n d / o r print any part of it, Residues present more than once can be grouped by enclosing them in square brackets and indicating the number of times they appear in the sequence. This extends the possibility of input which is limited in the current version by the length of the string that can be accepted (255 characters). The output provides the following information: sequence introduced, its molecular weight, the occurrence of each of the elements, and their weight percentage. The result can be directed to the printer if desired. In Fig. 1, a sample output of the program is shown. It is also possible to determine the same parameters on any molecule containing the elements listed above by introducing directly the number of atoms present.

0169-2607/89/$03.50 © 1989 ElsevierSciencePublishers B.V. (BiomedicalDivision)

120 boc-met - al~- lys ( z ) - [ val ] 3 -g lu*nh3Hol.Wt. = 1457.792 Type of Atom: Number of atoms: Percentage:

C 62 51 . 0 8

H 91 6.29

N 10 9.61

phe- opcp w[ h2o ] 2

0 17 18.66

8 1 2.20

F 0 O.O(J

(:1 5 12.16

Br 0 0.00

Fig. 1. Sample output showing the features of the program: (1) input including side-chain protecting groups, grouping of residues, crysta]l~a[Jon salts; (2) output including the molecular weight of the sequence introduced, the occurenc~ of each atomic species, and their weight percentage.

Although designed for peptide elemental analysis, it can be modified to suit any organic chemist's needs, by simply modifying the fibrary accordingly. The program is menu driven and easy to use. We run it on an Olivetti M24 (640 kbyte with a 10 Mbyte hard disk. When compiled, it takes approximately 10 s for the longest search possible. A listing a n d / o r copy of this program can be obtained sending a postage-paid envelope and a 5.25" floppy disk (double density) to the author.

Acknowledgements This work was supported by the Consiglio Nazionale delle Ricerche (C.N.R.) of Italy. References [1] M. Bodanszky, /n: Principles of Peptide Synthesis, p. 1 (Springer-Vedag, Berfin - Heidelberg - New York - Tokyo,

1984). [2] E. Wi~nsch, in: Houben-Weil Methoden der organischen Chemie, Band 15, Synthese yon Peptiden, Tell 2, p. 458 (Georg Thieme Verlag, Stuttgart, 1974).