P212121

The Birmingham News just reported that former researcher, H.M. Krishna Murthy, may have falsified or fabricated data. The Journal of Biological Chem­­istry has already retracted the paper in question, which contains PDB entry 1BEF.

If other journals follow suite the impact will be significant. According to Google Scholar, a total of 449 cite the papers in which these structures appear.

The University of Ala­bama at Birmingham announced that 12 structures were falsified or fabricated. The 12 questionable structures that have been deposited into the PDB are as follows: 1BEF, 1CMW, 1DF9, 2QID, 1G40, 1G44, 1L6L, 2OU1, 1RID, 1Y8E, 2A01, and 2HR0.

The publications involve a wide range of topics including: dengue viruses, serine proteases, Taq DNA polymerase, heparan sulfate proteoglycans, apolipoprotein A-II and A-I, suramin in heparin binding, and complement component 3.

The following table contains links to the structures, pdf of the journal articles and citations. The table is worth exploring if you believe you may draw conclusions based on these structures.

The process in macromolecular crystallography for generating heavy atom derivatives can be tedious. Problems may arise from heavy atoms not being incorporated into your protein to difficulty in producing crystals for derivatization trials therefore making each attempt critical.

The Heavy-Atom Database System: HATODAS II has been created to address these problems. The database uses 93 known heavy atom binding motifs (derived from 3103 heavy atom binding sites) and can take into account the amino acid sequence as well as the crystallization condition (ref).

Here is an example of a prediction that HASTODAS generates for potential heavy-atom reagents:

The following is a list of the suggested motifs that are present in the submitted sequence:

If your protein does not contain a His, Cys or Met then you maybe forced to mutate a residue for derivatization, but which one do you choose? HASTODAS addresses this question by suggesting a point mutation(s) based on multiple sequence alignments of homologous proteins.

Points for creating a database with guts.