This image shows how the cells of the C98RhuA crystal lattice are hinged at the corners of the C98RhuA tetramer, which can turn to open or close the pore. Image: Robert Alberstein et al.A team of chemists at the University of California, San Diego (UCSD) has designed a two-dimensional (2D) protein crystal that toggles between states of varying porosity and density. This is a first in biomolecular design, combining experimental studies with computation on supercomputers. The research, published in a paper in Nature Chemistry, could help create new materials for renewable energy, medicine, water purification and more.
"We did an extensive set of molecular dynamics simulations and experiments, which explained the basis of the unusual structural dynamics of these artificial proteins, based on which we were able to make rational decisions and alter the structural dynamics of the assembly," said study co-author Akif Tezcan, a professor of chemistry and biochemistry at UCSD.
Tezcan's team worked with the protein L-rhamnulose-1-phosphate aldolase (RhuA), which they modified with cysteine amino acids at position 98 to create C98RhuA. The team had previously published work on the self-assembly of this artificial, 2D protein architecture, which Tezcan said showed an interesting behavior called auxeticity.
"These crystalline assemblies can actually open and close in coherence," he said. "As they do, they shrink or expand equally in X and Y directions, which is the opposite of what normal materials do. We wanted to investigate what these motions are due to and what governs them." An example of auxeticity can be seen in the Hoberman Sphere, a toy ball that expands through its scissor-like hinges when you pull the ends apart.
"Our goal was to be able to do the same thing, using proteins as building blocks, to create new types of materials with advanced properties," Tezcan said. "The example that we're studying here was essentially the fruit of those efforts, where we used this particular protein that has a square-like shape, which we attached to one another through chemical linkages that were reversible and acted like hinges. This allowed these materials to form very well-ordered crystals that were also dynamic due to the flexibility of these chemical bonds, which ended up giving us these new, emergent properties."
By opening and closing the pores in the C98RhuA protein 2D lattices, specific molecular targets could be captured or released, which would be useful for drug delivery or the creation of better batteries, Tezcan said. Or the pores could selectively allow or block the passage of biological molecules for water filtration.
"Our idea was to be able to build complex materials, like evolution has done, using proteins as building blocks," Tezcan said.
To produce this protein-based material, Tezcan's team expressed the proteins in Escherichia coli cells and then purified them. Next, they induced the formation of the chemical linkages that actually create the crystals of C98RhuA, which vary as a function of their oxidation state, through the addition of redox-active chemicals.
"Once the crystals are formed, the big characterization becomes the openness or closeness of the crystals themselves," explained Tezcan. This was determined through statistical analysis of hundreds of images captured using electron microscopy.
The experiments worked hand-in-hand with computation, primarily all-atom simulations using software known as NAMD, which was developed at the University of Illinois at Urbana Champaign by the group of the late biophysicist Klaus Schulten.
To get to the bottom of how the crystal opens and closes, Tezcan's team employed a reduced system of just four proteins linked together, which can be tiled infinitely. "The reduced system allowed us to make these calculations feasible for us, because there are still hundreds of thousands of atoms, even in this reduced system," Tezcan said. His team took advantage of features specific to C98RhuA, such as using a single reaction coordinate corresponding to its openness. "We were really able to validate this model as being representative of what we observed in the experiment," Tezcan said.
The all-atom molecular simulations of the C98RhuA crystal lattices were used to map the free-energy landscape, which looks like a natural landscape, with valleys, mountains and mountain passes, explained study co-author Francesco Paesani, a professor of chemistry and biochemistry at UCSD. "The valleys become the most stable configurations of your protein assemblies," he said, which the molecular system prefers over having to spend energy to go over a mountain. And the mountain passes show the way from one stable structure to another.
"Typically, free energy calculations are very expensive and challenging because essentially what you're trying to do is sample all possible configurations of a molecular system that contains thousands of atoms. And you want to know how many positions these atoms can acquire during a simulation. It takes a lot of time and a lot of computer resources," Paesani said.
To meet these and other computational challenges, Paesani has been awarded supercomputer allocations through the Extreme Science and Engineering Discovery Environment (XSEDE), funded by the US National Science Foundation.
"Fortunately, XSEDE has provided us with an allocation on Maverick, the GPU computing clusters at the Texas Advanced Computing Center (TACC)," Paesani said. Maverick is a dedicated visualization and data analysis resource architected with 132 NVIDIA Tesla K40 ‘Atlas’ graphics processing units (GPU) for remote visualization and GPU computing to the national community.
"That was very useful to us, because the NAMD software that we use runs very well on GPUs. That allows us to speed up the calculations by orders of magnitudes," Paesani said. "Nowadays, we can afford calculations that 10 years ago we couldn't even dream about because of these developments, both on the NAMD software and on the hardware. All of these computing clusters that XSEDE provides are actually quite useful for all molecular dynamic simulations."
Through XSEDE, Paesani used several supercomputing systems, including: Gordon, Comet and Trestles at the San Diego Supercomputer Center; Kraken at the US National Institute for Computational Sciences; and Ranger, Stampede and Stampede2 at TACC.
"Because all the simulations were run on GPUs, Maverick was the perfect choice for this type of application," Paesani said.
Computation and experiment worked together to produce results. "I think this is a beautiful example of the synergy between theory and experiment," Paesani said. "Experiment posed the first question. Theory and computer simulation addressed that question, providing some understanding of the mechanism. And then we used computer simulation to make predictions and ask the experiments to test the validity of these hypotheses. Everything worked out very nicely because the simulations explained the experiments at the beginning. The predictions that were made were confirmed by the experiments at the end. It is an example of the perfect synergy between experiments and theoretical modeling."
"Chemists traditionally like to build complex molecules from simpler building blocks, and one can envision doing such a combination of design, experiment and computation for smaller molecules to predict their behavior," said Tezcan. "But the fact that we can do it on molecules that are composed of hundreds of thousands of atoms is quite unprecedented."
The science team also used molecular dynamics simulations to rigorously investigate the role of water in directing the lattice motion of C98RhuA. "This study showed us how important the active role of water is in controlling the structural dynamics of complex macromolecules, which in biochemistry can get overlooked," Tezcan explained. "But this study showed, very clearly, that the dynamics of these proteins are driven actively by water dynamics, which I think brings the importance of water to the fore."
"At the heart of this research is understanding how the properties of materials arise from the underlying molecular or atomic structure," said Rob Alberstein, graduate student in the Tezcan group and first author of the Nature Chemistry paper. "It's very difficult to describe. In this case we really sought to draw that connection as clearly as we could understand it ourselves and really show not only as from the experiment, where we can look at the macroscale behavior of these materials, but then with the computation relate that behavior back to what is actually going on at the scale of molecules. As we continue to develop as a society, we need to develop new materials for new sorts of global issues (water purification, etc), so understanding this relationship between atomic structure and the material property itself and the ability to predict those is going to become increasingly important."
This story is adapted from material from the Texas Advanced Computing Center, with editorial changes made by Materials Today. The views expressed in this article do not necessarily represent those of Elsevier. Link to original source.