Abstract
Since 1929 the concept that proteins are built from subunits of certain standard size (Svedberg 1929) has been revisited several times, each time with a new demonstration that, indeed, there are certain preferred protein sizes. According to recent estimates the overrepresented sizes are close to multiples of 125 amino acid (aa) residues for eukaryotes and 150 residues for prokaryotes. To explain these preferences, a hypothesis is suggested, and quantitatively developed, on the recombinational nature of this regularity. The protein-coding sequences are assumed to evolve at some early stage via recombinational events—insertions of DNA circles of a certain optimal size. The contour lengths of the protein-coding DNA circles had to be simultaneously divisible by three and, to minimize torsional constraint, by the DNA helical repeat. With these two conditions satisfied, the calculated contour lengths of the DNA circles, 250–500 base pairs (bp), turn out to correspond well to known optimal DNA circularization sizes and to the predicted range of the protein sequence subunit sizes: 80–170 as residues, which covers experimentally observed values. The subunit size is found to be strongly influenced by the helical repeat of DNA. The sizes 125 and 150 as are derived when the corresponding helical repeats of DNA are set within fractions of promilles from the 10.54 by/turn value. This fits to the experimentally estimated mean for natural mixed DNA sequences, 10.53–10.57 by/turn. The suggested recombinational mechanism thus not only gives a qualitative explanation for the observed underlying order in the protein sequences but also quantitatively links the observed protein sequence sizes with the optimal DNA circularization size and with the helical repeat of DNA. It also offers a versatile molecular model of early protein evolution by fusion and insertion of preexisting proteins of standard subunit sizes.
Article PDF
Similar content being viewed by others
Avoid common mistakes on your manuscript.
References
Berman AL, Kolker E, Trifonov EN (1994) Underlying order in protein sequence organization. Proc Natl Acad Sci USA (in press)
Diekmann S, Wang JC (1985) On the sequence determinants and flexibility of the kinetoplast DNA fragment with abnormal gel electrophoretic mobilities. J Mol Biol 186:1–11
Goulet I, Zyvanovic Y, Prunell A (1987) Helical repeat of DNA in solution. The V curve method. Nucleic Acids Res 15:2803–2821
Horowitz DS, Wang JC (1984) Torsional rigidity of DNA and length dependence of the free energy of DNA supercoiling. J Mol Biol 173:75–91
Kabsch W, Sander C, Trifonov E (1982) The ten helical twist angles of B-DNA. Nucleic Acids Res 10:1097–1104
Maniatis T (1991) Mechanisms of alternative pre-mRNA splicing. Science 251:33–34
Pascarella S, Argos P (1992) Analysis of insertions/deletions in protein structures. J Mol Biol 224:461–471
Peck LJ, Wang JC (1981) Sequence dependence of the helical repeat of DNA in solution. Nature 292:375–378
Savageau MA (1986) Proteins of Escherichia coli come in sizes that are multiples of 14 kDa: domain concepts and evolutionary implications. Proc Natl Acad Sci USA 83:1198–1202
Shub DA, Goodrich-Blair H (1992) Protein introns: a new home for endonucleases. Cell 71:183–186
Shimada J, Yamakawa H (1984) Ring-closure probabilities for twisted wormlike chains. Application to DNA. Macromolecules 17:689–698
Shore D, Baldwin RL (1983a) Energetics of DNA twisting. I. Relation between twist and cyclization probability. J Mol Biol 170:957–981
Shore D, Baldwin RL (1983b) Energetics of DNA twisting. II. Topoisomer analysis. J Mol Biol 170:983–1007
Strauss F, Gaillard C, Prunell A (1981) Helical periodicity of DNA, poly(dA) · poly(dT) and poly(dA-dT) · poly(dA-dT) in solution. Eur J Biochem 118:215–222
Svedberg T (1929) Mass and size of protein molecules. Nature 123:871
Svedberg T (1937) The ultra-centrifuge and the study of high-molecular compounds. Nature 139:1051–1062
Zuckerkandl E (1975) The appearance of new structures and functions in proteins during evolution. J Mol Evol 7:1–57
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Trifonov, E.N. On the recombinational origin of protein-sequence-subunit structure. J Mol Evol 38, 543–546 (1994). https://doi.org/10.1007/BF00178853
Received:
Accepted:
Issue Date:
DOI: https://doi.org/10.1007/BF00178853