Posted in | Quantum Physics

Creating Biomolecular Design by Combining Experiments with Supercomputing

From where does Kevlar get the ability to stop a bullet, at the atomic level? The atomic or molecular structure materials are responsible for their properties; however, various details between the micro and the macro have remained obscure to the field of science. Researchers are now actively studying the rational design of targeted supramolecular architectures to be able to manipulate their structural dynamics and their reaction to environmental cues.

Chemists at the University of California, San Diego (UCSD) designed a sheet of proteins (C98RhuA) that toggle between different states of porosity and density. The cells of the crystal lattice are hinged at the corners of the C98RhuA tetramer, allowing it to turn and open or close the pore. (Image credit: Robert Alberstein et al.)

At present, chemists from the University of California, San Diego (UCSD) have developed a two-dimensional protein crystal that switches between states that have different densities and porosities. This is the first ever biomolecular design created by combining experimental studies with computation on supercomputers. The study was reported in Nature Chemistry in April 2018 and could pave the way for developing innovative materials for water purification, medicine, renewable energy, and much 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.

Akif Tezcan, Co-Author & Professor of Chemistry & Biochemistry at UCSD

Tezcan and his colleagues modified the protein L-rhamnulose-1-phosphate aldolase (RhuA) by using cysteine amino acids in its four corners at position 98 (C98RhuA). Earlier he and his team had published a study on the self-assembly of this artificial, two-dimensional protein architecture, which according to him exhibited a fascinating behavior termed auxeticity.

These crystalline assemblies can actually open and close in coherence,” stated Tezcan. “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 is observed in the Hoberman Sphere, a toy ball that expanding with the help of its scissor-like hinges when the ends are pulled 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. 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.

Akif Tezcan, Co-Author & Professor of Chemistry & Biochemistry at UCSD

According to Tezcan, when the opening and closing of pores in the 2D lattices of the C98RhuA protein are controlled, it could lead to capture or release of certain molecular targets helpful for drug delivery or development of more efficient batteries with further studies. Otherwise, they could even selectively progress through or block the passage of biological molecules and filter water.

Our idea was to be able to build complex materials, like evolution has done, using proteins as building blocks,” stated Tezcan.

Tezcan and his colleagues achieved this by first expressing the proteins in Escherichia coli bacteria cells and purify them. Following this, they coaxed the formation of the chemical linkages that in fact form the crystals of C98RhuA. These linkages vary as a function of their oxidation state, with the addition of redox-active chemicals.

Once the crystals are formed, the big characterization becomes the openness or closeness of the crystals themselves,” elucidated Tezcan, which was ascertained by performing statistical analysis of hundreds of images captured with the help of electron microscopy.

The experiments were carried out in tandem with computation, mainly all-atom simulations with the help of the NAMD software created at the University of Illinois at Urbana Champaign by the team of the late biophysicist Klaus Schulten.

Tezcan and his colleagues used a reduced system of only four proteins connected together, which can be infinitely tiled to get a better picture of the way the crystal opens and closes.

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,” stated Tezcan. His team made the most of the properties that are specific to C98RhuA, for instance, the use of a single reaction coordinate consistent with its openness.

We were really able to validate this model as being representative of what we observed in the experiment,” stated Tezcan.

The free-energy landscape was mapped by using the all-atom molecular simulations of the C98RhuA crystal lattices. With mountains, mountain passes, and valleys, this landscape resembles a natural landscape, elucidated Francesco Paesani, co-author of the study, who is a professor of chemistry and biochemistry at UCSD.

The valleys become the most stable configurations of your protein assemblies,” stated Paesani, preferred by the molecular system rather than spending energy to move over a mountain. Moreover, the mountain passes exhibit the way from one stable structure to the other.

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,” stated Paesani.

Paesani was awarded supercomputer allocations through XSEDE, the Extreme Science and Engineering Discovery Environment, funded by the National Science Foundation, to overcome these and other computational challenges.

Fortunately, XSEDE has provided us with an allocation on Maverick, the GPU computing clusters at the Texas Advanced Computing Center (TACC),” stated Paesani. Designed with 132 NVIDIA Tesla K40 “Atlas” graphics processing units (GPU) for remote visualization and GPU computing for the national community, Maverick is a dedicated visualization and data analysis resource.

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,” stated Paesani. “Nowadays, we can afford calculations that ten 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.”

XSEDE helped Paesani to use a number of supercomputing systems, such as Trestles, Comet, and Gordon at the San Diego Supercomputer Center; Kraken at the National Institute for Computational Sciences; and Stampede, Stampede2, and Ranger at TACC.

Because all the simulations were run on GPUs, Maverick was the perfect choice for this type of application,” stated Paesani.

Computation and experiment worked together to produce results.

I think this is a beautiful example of the synergy between theory and experiment. 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.

Francesco Paesani, Co-Author

Tezcan further stated that “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. But the fact that we can do it on molecules that are composed of hundreds of thousands of atoms is quite unprecedented.”

The team of researchers also adopted molecular dynamics simulations for a thorough analysis of the role of water in initiating 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,” stated Tezcan. “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. 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.

Rob Alberstein, Graduate Student on Tezcan’s team & First Author

The study titled “Engineering the entropy-driven free-energy landscape of a dynamic nanoporous protein assembly” (doi:10.1038/s41557-018-0053-4) was published in the Nature Chemistry journal in April 2018. The authors of the study are Robert Alberstein, Yuta Suzuki, Francesco Paesani, and F. Akif Tezcan from the University of California, San Diego. The study was funded by the US Department of Energy Award DE-SC0003844 and by the National Science Foundation through grant CHE-1453204. All computer simulations were performed on the NSF-funded Extreme Science and Engineering Discovery Environment through grant ACI-1053575.

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