Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

TSRI Scientists Create New Tool for Exploring Cells in 3D

02.12.2014

As Proof-of-Principle, Model Provides Insight into HIV Structure

Researchers can now explore viruses, bacteria and components of the human body in more detail than ever before with software developed at The Scripps Research Institute (TSRI).


The new software can generate editable models of mid-size biological structures such as this one of HIV. (Image created by Graham Johnson and Ludovic Autin of The Scripps Research Institute.)

In a study published online ahead of print December 1 by the journal Nature Methods, the researchers demonstrated how the software, called cellPACK, can be used to model viruses such as HIV.

“We hope to ultimately increase scientists’ ability to target any disease,” said Art Olson, professor and Anderson Research Chair at TSRI who is senior author of the new study.

Putting cellPACK to the Test

The cellPACK software solves a major problem in structural biology. Although scientists have developed techniques to study relatively large structures, such as cells, and very small structures, such as proteins, it has been harder to visualize structures in the medium “mesoscale” range.

With cellPACK, researchers can quickly and efficiently process the data they’ve collected on smaller structures to assemble models in this mid-size range. Previously, researchers had to create these models by hand, which took weeks or months compared with just hours in cellPACK.

As a demonstration of the software’s power, the authors of the new study created a model of HIV showing how outer “spike” proteins are distributed on the surface of the immature virus.

The new model put to the test a conclusion made by HIV researchers from super-resolution microscopic studies—that the distribution of the spike proteins on the surface of the immature virus is random. But by using cellPACK to generate thousands of models, testing alternative hypotheses, the researchers found that the distribution was not random. “We demonstrated that their interpretation of the distribution did not match that hypothesis,” said Olson.

A Team Effort

The cellPACK software began as the thesis project of a TSRI graduate student, Graham Johnson, now a QB3 faculty fellow at the University of California, San Francisco (UCSF) who continues to contribute to the project. Johnson had more 15 years’ experience as a medical illustrator, and he wanted to create an easy way to visualize mesoscale structures. cellPACK is an expansion of Johnson’s autoPACK software, which maps out the density of materials—from concrete in a building to red blood cells in an artery.

The researchers see cellPACK as a community effort, and they have made the autoPACK and cellPACK software free and open source. Thousands of people have already downloaded the software from http://www.autopack.org .

“With the creation of cellPACK, Dr. Olson and his colleagues have addressed the challenge of integrating biological data from different sources and across multiple scales into virtual models that can simulate biologically relevant molecular interactions within a cell,” said Veersamy Ravichandran, PhD, of the National Institutes of Health's National Institute of General Medical Sciences, which partially funded the research. “This user-friendly tool provides a new platform for data analysis and simulation in a collaborative manner between laboratories.”

As new information comes in from the scientific community, researchers will tweak the software so it can model new shapes. “Making it open source makes it more powerful,” said Olson. “The software right now is usable and very useful, but it’s really a tool for the future.”

In addition to Olson and Johnson, other authors of the study, “cellPACK: A Virtual Mesoscope to Model and Visualize Structural Systems Biology,” are Ludovic Autin, Mostafa Al-Alusi, David S. Goodsell and Michel F. Sanner, all of TSRI. For more information, see http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.3204.html

This study was supported by the National Science Foundation (NSF 07576), Autodesk, the National Institutes of Health (P41 GM103426 and P50GM103368), the California Institute for Quantitative Biosciences and a UCSF School of Pharmacy 2013 Mary Anne Koda-Kimble Seed Award for Innovation.

About The Scripps Research Institute

The Scripps Research Institute (TSRI) is one of the world's largest independent, not-for-profit organizations focusing on research in the biomedical sciences. TSRI is internationally recognized for its contributions to science and health, including its role in laying the foundation for new treatments for cancer, rheumatoid arthritis, hemophilia, and other diseases. An institution that evolved from the Scripps Metabolic Clinic founded by philanthropist Ellen Browning Scripps in 1924, the institute now employs about 3,000 people on its campuses in La Jolla, CA, and Jupiter, FL, where its renowned scientists—including two Nobel laureates—work toward their next discoveries. The institute's graduate program, which awards PhD degrees in biology and chemistry, ranks among the top ten of its kind in the nation. For more information, see www.scripps.edu  .

For information:
Office of Communications
Tel: 858-784-2666
Fax: 858-784-8136
press@scripps.edu

Madeline McCurry-Schmidt | EurekAlert!
Further information:
http://www.scripps.edu/news/press/2014/20141201olson.html

Further reports about: Cells TSRI UCSF data analysis immature proteins red blood cells rheumatoid arthritis structures viruses

More articles from Life Sciences:

nachricht At last, butterflies get a bigger, better evolutionary tree
16.02.2018 | Florida Museum of Natural History

nachricht New treatment strategies for chronic kidney disease from the animal kingdom
16.02.2018 | Veterinärmedizinische Universität Wien

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Demonstration of a single molecule piezoelectric effect

Breakthrough provides a new concept of the design of molecular motors, sensors and electricity generators at nanoscale

Researchers from the Institute of Organic Chemistry and Biochemistry of the CAS (IOCB Prague), Institute of Physics of the CAS (IP CAS) and Palacký University...

Im Focus: Hybrid optics bring color imaging using ultrathin metalenses into focus

For photographers and scientists, lenses are lifesavers. They reflect and refract light, making possible the imaging systems that drive discovery through the microscope and preserve history through cameras.

But today's glass-based lenses are bulky and resist miniaturization. Next-generation technologies, such as ultrathin cameras or tiny microscopes, require...

Im Focus: Stem cell divisions in the adult brain seen for the first time

Scientists from the University of Zurich have succeeded for the first time in tracking individual stem cells and their neuronal progeny over months within the intact adult brain. This study sheds light on how new neurons are produced throughout life.

The generation of new nerve cells was once thought to taper off at the end of embryonic development. However, recent research has shown that the adult brain...

Im Focus: Interference as a new method for cooling quantum devices

Theoretical physicists propose to use negative interference to control heat flow in quantum devices. Study published in Physical Review Letters

Quantum computer parts are sensitive and need to be cooled to very low temperatures. Their tiny size makes them particularly susceptible to a temperature...

Im Focus: Autonomous 3D scanner supports individual manufacturing processes

Let’s say the armrest is broken in your vintage car. As things stand, you would need a lot of luck and persistence to find the right spare part. But in the world of Industrie 4.0 and production with batch sizes of one, you can simply scan the armrest and print it out. This is made possible by the first ever 3D scanner capable of working autonomously and in real time. The autonomous scanning system will be on display at the Hannover Messe Preview on February 6 and at the Hannover Messe proper from April 23 to 27, 2018 (Hall 6, Booth A30).

Part of the charm of vintage cars is that they stopped making them long ago, so it is special when you do see one out on the roads. If something breaks or...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

VideoLinks
Industry & Economy
Event News

2nd International Conference on High Temperature Shape Memory Alloys (HTSMAs)

15.02.2018 | Event News

Aachen DC Grid Summit 2018

13.02.2018 | Event News

How Global Climate Policy Can Learn from the Energy Transition

12.02.2018 | Event News

 
Latest News

Fingerprints of quantum entanglement

16.02.2018 | Information Technology

'Living bandages': NUST MISIS scientists develop biocompatible anti-burn nanofibers

16.02.2018 | Health and Medicine

Hubble sees Neptune's mysterious shrinking storm

16.02.2018 | Physics and Astronomy

VideoLinks
Science & Research
Overview of more VideoLinks >>>