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. (Credit: Robert Alberstein et al.)

What makes kevlar stop a bullet, at the atomic level?

The properties of materials emerge from their molecular or atomic structure, yet many details between the micro and the macro remain a mystery to science. Scientists are actively researching the rational design of targeted supramolecular architectures, with the goal of engineering their structural dynamics and their response to environmental cues.

A team of chemists at the University of California, San Diego (UCSD) has now designed a two-dimensional protein crystal that toggles between states of varying porosity and density. This is a first in biomolecular design that combined experimental studies with computation done on supercomputers. The research, published in April 2018 in Nature Chemistry, could help create new materials for renewable energy, medicine, water purification, and more.

Structural features of C98RhuA crystals. a, Surface representation of a C98RhuA tetramer, with position 98 highlighted in black, and a schematic of its oxidative self-assembly into porous 2D crystals. b, TEM images and cartoon representations of the conformational states accessible by C98RhuA lattices and their respective ξ values. Scale bars: 50 nm. c, Schematic of the 'interaction belt' (± 10 Å of residue 98), which protrudes from the protein. Slice views are of this belt region as viewed normal to the crystal. d, Overview of the calculation of the parameter E from experimental measurements and its generalization to the coordinate ξ. The measured parameters and their converted values are reported for each example. (Credit: Robert Alberstein et al.)

"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.

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

Francesco Paesani, Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla.

"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."

All of these computing clusters that XSEDE provides are actually quite useful for all molecular dynamic simulations.

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

F. Akif Tezcan, Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla.

"Once the crystals are formed, the big characterization becomes the openness or closeness of the crystals themselves," explained Tezcan, which 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 the NAMD software developed at the University of Illinois at Urbana Champaign by the group of the late biophysicist Klaus Schulten.

Tezcan's team used a reduced system of just four proteins linked together, which can be tiled infinitely to get to the bottom of how 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," 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.

Robert Alberstein, Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla.

"The valleys become the most stable configurations of your protein assemblies," Paesani 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 XSEDE, the Extreme Science and Engineering Discovery Environment, funded by the National Science Foundation.

Simulated reconstruction of the dynamic motions of C98RhuA crystals. The video was constructed by taking transmission electron microscopy images of C98RhuA crystals at different conformations, and interpolating between the different states, an entropically-driven process. (Credit: Robert Alberstein et al.)

"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 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."

Through XSEDE, Paesani used several supercomputing systems, including Gordon, Comet, and Trestles at the San Diego Supercomputer Center; Kraken at the 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.

A Hoberman sphere is an isokinetic structure that resembles a geodesic dome, but is capable of folding down to a fraction of its normal size by the scissor-like action of its joints. (Credit: Wikipedia, Florian Karsten)

Tezcan added 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 Maverick supercomputer is a dedicated visualization and data analysis resource at the Texas Advanced Computing Center that's architected with 132 NVIDIA Tesla K40 "Atlas" graphics processing units (GPU) for remote visualization and GPU computing to the national community.

Chemical and mechanical switching behaviour of CEERhuA crystals. a, Top: schematic depicting all of the possible switching modes of CEERhuA lattices. Bottom: experimental distribution(s) corresponding to the states directly above. The addition of 20 mM Ca2+ to the equilibrium 'ajar' population of CEERhuA crystals induced a shift towards more closed conformations, from which C98RhuA-like mechanical switching was possible. The ajar conformation was fully recoverable upon removal of the Ca2+ via dialysis or EDTA, thus providing three distinct switching modes. Gaussian fits to each distribution are labelled with their centre (c) and s.d. (σ). n is the number of crystals analysed. The lattice conformation of each inset is marked with an asterisk. b, Summary of switching modes for RhuA crystals. In contrast with C98RhuA, CEERhuA has two mechanical modes dictated by the presence of Ca2+, as well as a purely chemical mode via the addition or removal of Ca2+. (Credit: Robert Alberstein et al.)

The study, "Engineering the entropy-driven free-energy landscape of a dynamic nanoporous protein assembly," (doi:10.1038/s41557-018-0053-4) was published in April of 2018 in the journal Nature Chemistry. The authors are Robert Alberstein, Yuta Suzuki, Francesco Paesani, and F. Akif Tezcan of the University of California, San Diego. Funding was provided 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.