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Computational Virus Simulation Offers Promise


A team of computational biologists at the University of Illinois at Urbana-Champaign has performed an all-atom molecular dynamics simulation of the satellite tobacco mosaic virus — marking the first computational simulation of an entire life form and a potential advance for computational drug design.

The simulation, described in the March issue of the journal Structure, tracked the dynamics of the complete virus — comprising a 60-protein icosahedral capsid and a 1.1 kb RNA core — for 13 nanoseconds. The researchers also performed several 10-ns simulations of the capsid and the RNA alone, reaching the conclusion that the capsid is unstable and “implodes” when the RNA core is not present.

Previous experimental evidence had hinted at this behavior for STMV, which contradicts the “prevalent view” that all viruses assemble by first forming a rigid shell and then pull in the genetic material, says Klaus Schulten, director of the Theoretical and Computational Biophysics Group at the University of Illinois and a co-author on the paper.

“In this particular case, it’s the opposite,” Schulten says. Based on the simulation, it appears that STMV “first forms the RNA, it folds into some fuzzy ball, and then that recruits one by one the 60 proteins to build the shell around itself.”

Schulten says that the simulation helps reinforce the experimental data, and serves as an example of how computing is becoming “a partner of experimental biology” and a useful tool for hypothesis generation in its own right.

Schulten says that his team chose STMV because of its small size. The entire simulation involved around 1 million atoms, which is near the upper limit of current molecular dynamics studies in biology.

The largest biological simulation to date was published last fall by researchers at Los Alamos National Laboratory, who simulated the behavior of 2.64 million atoms in the ribosome.

— Bernadette Toner

Short reads

NIH issued an RFA called “A Data Coordination Center for the Model Organism ENCODE Project” to invite proposals to implement a data coordination center for modENCODE, the ENCODE (Encyclopedia of DNA Elements) project for model organisms. NIH said it will award $1.5 million per year for three years to a single center. Letters of intent from interested organizations are due June 21 and applications are due July 21.

Stratagene will pay Strand Life Sciences roughly $4 million during the next two years as part of a software development collaboration begun late last year.

Johnson & Johnson Pharmaceutical Research & Development agreed to extend its research collaboration with Entelos for five more years. Under the deal, Entelos engineers and scientists will use their PhysioLab platforms to study multiple therapeutic areas.

The National Resource for Biomedical Supercomputing at the Pittsburgh Supercomputing Center will host a workshop called “Computational Methods for Spatially Realistic Microphysiological Simulations” from June 6-9.

Ingenuity Systems’ pathway analysis tool has garnered attention lately. The company announced a new licensee, the Pritzker Neuropsychiatric Disorders Research Consortium, as well as an expanded agreement with Sanofi-Aventis. Meanwhile, Ingenuity and Inpharmatica worked out a co-marketing deal for their software products.


US Patent 7,016,787. Characterizing biological stimuli by response curves. Inventors: Eugeni Vaisberg, Donald Oestreicher, Cynthia Adams. Assignee: Cytokinetics. Issued: March 21, 2006.

This patent covers “a method for generating stimulus response curves (e.g., dose response curves)” that illustrate “how the phenotype of one or more cells change in response to varying levels of the stimulus,” according to the abstract. “Such features often include basic parameters obtained from images (e.g., cell shape, nucleus area, Golgi texture) and/or biological characterizations derived from the basic parameters (e.g., cell cycle state, mitotic index, etc.).”

US Patent 7,016,786. Statistical methods for analyzing biological sequences. Inventors: Rama Ranganathan, Steve Lockless. Assignee: Board of Regents, The University of Texas System. Issued: March 21, 2006.

According to the abstract, this invention includes “statistical algorithms that are useful to aid in the identification of evolutionarily conserved amino acid positions within a family of proteins, and in the identification of interacting amino acid positions within a protein sequence.”



Accelrys announced plans to lay off 50 employees, or about 10 percent of its staff, before the end of June. The layoffs will be split between the company’s facilities in the US and Europe, with no cuts planned for the Asia-Pacific region.

The Scan

Self-Reported Hearing Loss in Older Adults Begins Very Early in Life, Study Says

A JAMA Otolaryngology — Head & Neck Surgery study says polygenic risk scores associated with hearing loss in older adults is also associated with hearing decline in younger groups.

Genome-Wide Analysis Sheds Light on Genetics of ADHD

A genome-wide association study meta-analysis of attention-deficit hyperactivity disorder appearing in Nature Genetics links 76 genes to risk of having the disorder.

MicroRNA Cotargeting Linked to Lupus

A mouse-based study appearing in BMC Biology implicates two microRNAs with overlapping target sites in lupus.

Enzyme Involved in Lipid Metabolism Linked to Mutational Signatures

In Nature Genetics, a Wellcome Sanger Institute-led team found that APOBEC1 may contribute to the development of the SBS2 and SBS13 mutational signatures in the small intestine.