The Center for Protein Structure and Function was established in 2000 with a $9.6 million grant from the US National Institutes of Health National Center for Research Resources.

Support for the Center was continued in 2005 with $10.2 million grant from NIH NCRR, as well as numerous other grants. The members of the University of Arkansas COBRE Center for Protein Structure and Function seek to make significant contributions to this fundamental understanding through multidisciplinary research projects using state-of-the-art techniques and instrumentation.

THE WORK THAT PROTEINS DO

Proteins do nearly all the work in the cells of our bodies, ranging from brain function and nerve transmission to metabolic energy production and muscular contraction. Moreover, most diseases are associated with defects in protein function.

Future advances in the understanding, diagnosis and treatment of human disease will depend upon better understanding of the structures, functions and interactions of the thousands of proteins that are encoded within the genomes of humans, and human pathogens. Such understanding will emerge from detailed investigations of the molecular structure and function of proteins that play an important role in human disease.

THE LONG SEARCH

“Thanks to funding from the National Institute of Health, which has supported our Center for a dozen years, we have superb instrumentation. However, protein structures are very large, making them hard to understand in 2D. I knew what I wanted and I knew want I needed. I tried hard to find the solution”
Dr. James Hinton, Professor at The Center for Protein Structure and Function

Dr. Hinton’s search for the missing link that would allow him to visualise in 3D was lengthy.

PYMOL 3D

PyMOL renders publication-quality illustrations of macromolecules, including drug targets. Molecular animations can be created through simple object and camera motions or through input of trajectories from molecular dynamics simulations and other dynamic conformational ensembles. Available molecular representations for nanotechnology pictures include space-filling “CPK” atoms, chemical bonds, cartoon ribbons, molecular surfaces, and solvent accessible surface meshes.

“Increasing numbers of our customers hail from the biochemistry and life sciences fields.  They asked us to create this plug-in to enhance the usability of PyMOL for them.  We worked with the product’s late creator, Warren DeLano, to add 3D tracking functionality to the software.”
Steve Carpenter, Virtalis’ PyMOL specialist

As a stereochemistry viewer, PyMOL can illustrate the 3D stereochemical relationships of organic chemistry. When viewing crystallographic protein structures, PyMOL can display millions of atoms inside a crystal lattice. Molecular interactions can be represented using interatomic distances, van der Waal’s clashes, property-based, potential-based and proximity-based colouring schemes, solid and mesh isosurface potentials, slice planes, and gradient field lines.

PyMOL also supports input of electron density maps, electrostatic potential maps, and other volumetric data sets, as well as arbitrary 3D geometries comprised of triangles, spheres, cylinders, cones, ellipsoids, and text.

ACTIVEMOVE

ActiveMove is a transportable, interactive 3D visualisation system that is setting the industry benchmark for both price and performance. It combines best in class technology and is part of the Virtalis ActiveWorks family of 3D immersive visualisation solutions.

ActiveMove can’t be beaten for those users looking for a cost effective and transportable solution that can be quickly assembled for department presentations, marketing seminars, trade shows, training workshops or research programmes.

With ActiveMove, data can not only be visualised in stereoscopic 3D, but also the system enables full immersion and interaction, thanks to Virtalis’ integrated head and hand tracking solution. The user can navigate through the virtual world, pick and manipulate component parts in real time and make decisions on the fly.

ActiveMove comprises an active, stereoscopic, High Definition resolution, high brightness, high frame rate, three chip DLP projector with a rear projection screen in a dedicated enclosure, coupled with a PC, eyewear, head and hand tracking, installation and support. ActiveMove is transported in two, custom, wheeled cases specifically design for local and international shipping, making it easy to share between locations.

THE VIRTALIS PYMOL SOLUTION

ActiveMove and its PyMOL software plug-in enables the stereoscopic 3D viewing of PyMOL at the University of Arkansas.  The system allows staff and students at the Centre for Protein Function and Structure to be immersed in and interact with the VR environment.  Crucially for Dr. Hinton and his team, PyMOL 3D gives the ability to interact with chemical structures via a tracked, hand held device.

Virtalis’ VR plug-in for PyMOL removes the need to return to the keyboard and mouse to change the viewing direction or orientation, making the whole process of interacting with molecules faster and more natural. The user simply navigates around the environment using the controls on the hand held device and can look at the molecules from different directions and angles with enhanced spatial and depth perception.

“The VR enabling of PyMOL by Virtalis makes interacting with protein structures in the ActiveMove very easy. We use the National Protein Databank to obtain the structures and load this data into PyMOL. I already have several people trained to run the ActiveMove, but the system is so easy to use, I will be broadening its use further. Now we can see the intricate three-dimensional geometry of the folded protein structures. Using movies made with this system, we are able to study protein-protein interaction and docking of proteins with small molecules for the examination of binding sites and how changes in the small molecule affect the binding process.”
Dr. James Hinton, Professor at The Center for Protein Structure and Function

BEYOND RESEARCH

The team at The University of Arkansas has already broadened the use of its Virtalis system beyond the research arena. It is being routinely used for teaching both graduate and undergraduate students and has even been deployed as a recruiting tool for the Department.

“People are rather blasé when I introduce the system, but I wait for the inevitable gasps that follow as they see its power. This is usually followed by laughter as they experience something they hadn’t expected.”
Dr. James Hinton, Professor at The Center for Protein Structure and Function