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Fraudulent database entries raise questions about protocol

Tracy Vence

Five months ago, the University of Alabama at Birmingham requested that 11 questionable structures be removed from the Research Collaboratory for Structural Bioinformatics Protein Data Bank. Today, the majority of the structures remain.

Six months ago, a panel at the University of Alabama at Birmingham (UAB) accused H.M. Krishna Murthy of scientific misconduct, after allegations of fabrication and falsification in his work surfaced in 2007. A month later, UAB requested that the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) remove 11 questionable structures, co-authored by Murthy, from their database. Five months after this request, the majority of the structures remain on the RCSB PDB web site.

The RCSB PDB is an archive of information on the 3-D structures of large biological molecules, co-managed by researchers at Rutgers University, in New Jersey; the San Diego Supercomputer Center (SDSC) in California; and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego.

The UAB internal investigation of Murthy’s work ran from January 2007 through May 2009. Under UAB’s scientific integrity policy and the Department of Health & Human Services Office of Research Integrity (ORI) regulations, a panel of experts deemed to have no conflicting interests investigated claims that undermined the validity and credibility of Murthy’s protein structures 1BEF, 1CMW, 1DF9/2QID, 1G40, 1G44, 1L6L, 2OU1, 1RID, 1Y8E, 2A01, and 2HR0.

“The committee re-analyzed each structure alleged to have been fabricated, and found a preponderance of evidence that structures…were more likely than not falsified and/or fabricated,” UAB wrote in a public statement.

The Journal of Biological Chemistry (JBC) retracted the paper, “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,” co-authored by Murthy, on Dec. 4. Christine Zardecki, a research associate at Rutgers, told BioTechniques that following the formal retraction, the RCSB PDB removed the structures associated with that paper from the database during weekly maintenance on Tuesday. Two of the remaining structures in the PDB are derived from a September 2002 paper in Biochemistry, which UAB has contacted to request a correction.

Five of the structures were co-authored by Murthy before he was a UAB employee, and therefore were not investigated by the school’s expert panel. When asked whether the PDB must wait for a formal retraction to remove contested structures, Zardecki said that, to her knowledge, an issue like this “hasn’t really come up before.”

Kristi Lamont Ellis, director of internal communications and relations at UAB, told BioTechniques that the ORI has been notified of the Murthy probe, and that UAB provided a report of their findings, per policy. John E. Dahlberg, director of the ORI’s Division of Investigative Oversight (the department responsible for the monitoring and evaluation of investigations conducted at awardee and applicant institutions) could not confirm or deny that the agency had an open case against Murthy.

Lamont Ellis said that the UAB has contacted several journals to request corrections and/or retractions of nine papers Murthy has co-authored. An ISI Web of Knowledge author search revealed Murthy as an author on 11 papers under his UAB affiliation, including two in Nature, two in the Proceedings of the National Academy of Sciences (PNAS), and one in the Journal of Molecular Biology (JMB), among others.

It’s a lengthy process, Lamont Ellis said, which is complicated by the co-authorship of contested work. “With any retraction or correction request, we try to have consent from all authors/co-authors,” she said. “While consent by all makes the process easier, UAB will proceed on its own if necessary.”

Daniel Salsbury, managing editor of PNAS, told BioTechniques that UAB had just contacted the journal today about the issue. “It would be premature to issue a retraction or correction until the matter has been fully considered by ORI,” he said.

Murthy’s employment contract with UAB expired in February of this year, at which time the school “chose not to renew it,” Lamont Ellis said.