1 CRISCEB, Research Center of Computational and Biotechnological Sciences and 2 Department of Biochemistry and Biophysics, Second University of Naples, via Costantinopoli 16, 80138 Naples, Italy
Sir,
Petukhov and colleagues ask why we failed to cite a recent paper of theirs (Petukhov et al., 1997) on the same topic as dealt with in our paper `Helix stabilizing factors and stabilization of thermophilic proteins: an X-ray based study' (Facchiano et al., 1998
). For several reasons, it is not an unusual event for published articles not to be cited. For example, we could point out that an earlier version of our manuscript had been submitted on March 7, 1997, i.e., when the manuscript by Petukhov and colleagues was still under consideration. Nonetheless, we decided not to cite their article, even when we became aware of its publication. Reasons for this decision are outlined below.
It is our opinion that Petukhov and co-workers did what `double starred' researchers should never do, i.e. extract one sentence from its context and then draw arbitrary and, possibly, misleading conclusions. If they were to read carefully our incriminated sentence (p. 753, last paragraph), they would realize that the first part of that sentence (`Although several articles draw a comparison between mesophilic and thermophilic homologues, ...') aims to avoid specific acknowledgement of previous articles. As everybody knows, it is often impracticable to quote all pertinent work by others. For brevity's sake, it is usual in science to resort to such a kind of all-inclusive sentence. The second part of our sentence (`... an evaluation of helix stability, as well as an inventory of putative helix-stabilizing factors, has never been carried out.') absolutely cannot be extracted from its context, which makes clear that our analysis concerns only those homologues for both of which the X-ray structures are available. Furthermore, our paper reports on the occurrence of 10 putative helix stabilizing factors, both in mesophilic and in thermophilic homologues.
Petukhov and co-workers affirm that the assumptions made in their paper lead to conclusions very similar to those drawn by us. We think that the two papers resemble one another in the fact that the same procedure was used to calculate helix stability. We do not conclude that `... the enhancement of the energy balance of intrahelical interactions is one of the main mechanisms responsible for the conformational stability of thermophilic proteins at high temperature'. On the contrary, our conclusion is that helix stability favours thermophilic proteins with the highest sequence identity with mesophilic homologues, but the opposite happens when divergence between sequences increases. At a glance, the analysis of Petukhov and co-workers falls within the first category. As their analysis concerns four protein families, against 13 analysed by us, the only similarity appears to be ascribable to this reason, all the more so because the correspondence between sequence similarity and structural organization does not always hold (see NPC, CGT and PFK in our work). By the way, we wonder whether assumptions should have the right of priority over experimental data or whether, instead, it is better to make assumptions based on experimental evidence.
We believe that the above reasons are sufficient to justify our decision. Of course, we are well disposed to cite articles by Petukhov and colleagues in all our future publications on the same matter, if deemed pertinent.
Notes
3 To whom correspondence should be addressed
References
Facchiano,A.M., Colonna,G. and Ragone,R. (1998) Protein Engng, 11, 753760.[Abstract]
Petukhov,M., Kil,Y., Kuramitsu,S. and Lanzov,V. (1997) Proteins, 29, 309320.[ISI][Medline]
Received November 24, 1998; revised February 8, 1999; accepted February 8, 1999.