Nature retracts paper six years after it was flagged for fraud

Nature retracted a paper on protein structures today, six years after an investigation at the University of Alabama identified several structures that were “more likely than not falsified and/or fabricated” by one of the authors.

The paper came under scrutiny soon after it was published in 2006. A letter published in Nature that same year pointed out “physically implausible features in the structures it described.” That triggered the investigation at the University of Alabama, the result of which was published in 2009, identifying “nine publications related to the same protein structures that should be retracted from various scientific journals.” Everything was pinned on last author H.M. Krishna Murthy, who the investigation determined was “solely responsible for the fraudulent data.”

A 2009 Nature news article on the investigation declared that the “fraud is the largest ever in protein crystallography.”

We’re not sure what took Nature so long to retract the letter, titled “The structure of complement C3b provides insights into complement activation and regulation.” Here’s the note, which explains that not all the authors agreed to the retraction:

This Letter is retracted by Nature. This follows an investigation by the University of Alabama at Birmingham, Alabama, USA, of structures deposited into the Protein Data Bank under accession 2HR0 by H. M. Krishna Murthy. Co-authors who agree with the Retraction: A. Abdul Ajees, John E. Volanakis, Sthanam V. Narayana. Co-authors who do not support the Retraction: Girish J. Kotwal and H. M. Krishna Murthy. K. Gunasekaran has not responded. The report from the University of Alabama at Birmingham investigation is available at: http://www.uab.edu/reporterarchive/71570-uab-statement-on-protein-data-bank-issues.

The statement from that investigation called for the retraction of nine publications in total that

should be retracted from various scientific journals, and is making those journals aware of this matter.

The online-first version of the paper has been cited 7 times, and the print version has been cited 42 times, according to Thomson Scientific’s Web of Knowledge.

We spoke to co- author Sthanam V. Narayana, who works at UAB, by phone.

This is a pretty old story, I don’t know why Nature took so long. Nature asked us maybe two months back, do I have any comment or objection for retracting.

He told them that he would gladly see it retracted. We asked if he was surprised by the results of the investigation:

Of course. Naturally. He’s a fellow scientist, a reputable scientist, we never suspected anything wrong. the part we looked at, it looked alright to us.  We didn’t have any role in that part of the work.

We’ve found that four of the other papers from the investigation have been retracted. Murthy is the only author common to all of them:

• Crystal structure of Dengue virus NS3 protease in complex with a Bowman-Birk inhibitor: implications for flaviviral polyprotein processing and drug design published in the Journal of Molecular Biology, has been cited 76 times
  (retraction notice)

• Dengue virus NS3 serine protease. Crystal structure and insights into interaction of the active site with substrates by molecular modeling and structural analysis of mutational effects, published in the Journal of Biological Chemistry, cited 97 times (retraction notice)

• “Structure of Taq DNA polymerase shows a new orientation for the structure-specific nuclease domain,” cited 14 times, and “Crystallization, characterization and measurement of MAD data on crystals of dengue virus NS3 serine protease complexed with mung-bean Bowman-Birk inhibitor,” cited 4 times, both published in Acta Crystallographica Section D (retraction notice)

According to the university investigation, with regard to the now-retracted Nature paper:

No raw crystallographic data, data reduction output, or any other experimental records that would support the correctness of the structure of 2HR0, or demonstrate that this was an experimentally determined structure, were available for examination.

The Nature news article from 2009 explains how the investigation began:

When the structures were deposited in the PDB, Janssen immediately noticed discrepancies between Murthy’s and his own, including large ‘gaps’ in the lattice that were unusual in such a well resolved and ordered structure. Janssen and his supervisor, Piet Gros, enlisted two well known crystallographers, Randy Read of the University of Cambridge, UK, and Axel Brünger of Stanford University, California, to examine it. They agreed that Murthy’s structure seemed to be fake. The group sent a brief communication to Nature in December 2006 questioning the structure and forwarded their concerns to the University of Alabama.

In December, we noticed on ChemFeeds that the letter was listed as retracted:

At the time, a spokesperson for Nature told us that the paper hadn’t been retracted yet, and that

Nature does not comment on retractions that may or may not be under consideration.

We have reached out to Nature for further information, and to authors John Volanakis (who has retired from UAB), and Abdul Ajees Abdul Salam (Manipal University). We could not find contact information for Murthy. We’ll update this post with anything else we learn.

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