Comment on a paper by Facchiano et al. (1998)

M. Petukhov1, Y. Kil2 and V. Lanzov2

1 European Molecular Biology Laboratory, Heidelberg, 69012, Germany and 2 St Petersburg Institute of Nuclear Physics, Russian Academy of Sciences, Gatchina, 188350 St Petersburg, Russia

Sir,

We would like to attract your attention to the paper by Facchiano et al. (1998) that appeared recently in this journal. In this paper, based on a comparison of X-ray structures of several mesophilic and thermophilic analogues, the authors reported that protein thermostabilty is mainly due to enchanced stability of the protein {alpha}-helices. However, we were surprised to learn from the Introduction that `Although several articles draw a comparison between mesophilic and thermophilic homologues, an evaluation of helix stability, as well as an inventory of putative helix stabilizing factors, has never been carried out'. This is not true.

In fact, we recently published work (Petukhov et al., 1997Go) where, among several other findings, we reported a connection between protein thermostability and several helix stabilizing factors for four protein families, used in our study. Although the journal concerned is widely available, we were not sure whether the authors had read our paper before their own publication. Therefore, one of us sent a letter with a reprint of our paper, asking them somehow to correct this mistake. Unfortunately, we received a negative reply, claiming that although Facchiano et al. `were aware of the paper' they `do not think that we have anything to complain about'. The reason that justifies this, in their view, is that we made an assumption while they used X-ray data only to obtain the sequences of protein helices.

It is widely accepted in the scientific community that authors should acknowledge previous work of others who were dealing with similar problems even if they (the others) used different approaches or assumptions. In this particular case not only was the problem the same (relationship between helix stability and protein thermostability) but also Facchiano et al. partly used the same methods (AGADIR-based calculations) and, not surprisingly, came to very similar conclusions regarding most important stabilizing factors. Under these circumstances, it is really hard to understand why they did not reference our paper.

As for the assumptions made in our paper, we must note we do not know of a single scientific work that is free of assumptions! Curiously enough, the fact that Facchiano et al. came to similar conclusions is further evidence that our assumptions were correct. Our paper was published in a respected journal and was assigned two `dots' as a work of outstanding interest in a review published in Current Opinions in Structural Biology (Gilardi, 1998Go). Therefore, the conclusion made by the authors that our results can be ruled out because our analysis was based on sequence comparisons rather than X-ray data is their personal opinion only. This kind of thing, in our view, must be discussed in a paper, instead of making misleading statements that similar work `has never been carried out'.

References

Facchiano,A.M., Golonna,G. and Ragone,R. (1998) Protein Engng, 11, 753–760.[Abstract]

Petukhov,M., Kil,Y., Kuramitsu,S. and Lanzov,V. (1997) Proteins: Struct. Funct. Genet., 29, 309–320.[ISI][Medline]

Gilardi,G. (1998) Curr. Opin. Struct. Biol., 8, 5.

Received November 12, 1998; revised February 11, 1999; accepted February 11, 1999.





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