News

Researchers Find Enzymes Naturally Select their Own Polymer Sequences

Findings could impact fields like pharmaceutical development and industrial waste processing

As free-flowing enzymes travel amid a sea of polymers, a Northwestern Engineering team has found those enzymes prefer to join certain polymer sequences over others, a discovery that could lead to applications in a diverse array of fields ranging from nuclear waste processing to drug delivery.

“From all these batches of randomness, we discovered each particular enzyme selects a sequence it likes best,” said Monica Olvera de la Cruz, the Lawyer Taylor Professor of Materials Science and Engineering at Northwestern’s McCormick School of Engineering and Applied Science, who led the study. “That’s important because it sheds light on how we might design the composition of a batch of polymers, so they will disperse enzymes actively in non-biological environments.”

Monica Olvera de la Cruz

Authored by Olvera de la Cruz and two colleagues in McCormick’s Department of Materials Science and Engineering — senior research associate Trung Dac Nguyen and research assistant professor Baofu Qiao — the study, titled “Efficient encapsulation of proteins with random copolymers,” published today, June 11, in the Proceedings of the National Academy of Sciences.

Enzymes play a vital role in a range of chemical and biological processes by facilitating and directing biochemical reactions. Due to the limited solubility of some substrates in water, preserving and/or enhancing the catalytic capability of some enzymes in non-aqueous solutions is of increasing demand. However, most enzymes rapidly lose their chemical activity when exposed to non-biological environments, including organic solvents like toluene and tetrahydrofuran. While numerous enzyme stabilization strategies have been employed such as reverse engineering enzyme sequences, decorating enzymes with surfactants, or modifying the solvents, most of them are either limited to specific enzymes and solvents or cost ineffective.

Performing computer simulations at Quest, Northwestern’s high-powered computational facility, the researchers examined: the key factors that determined the coverage of the random copolymers with different types of enzymes in a given solvent; how the enzymes selected the random copolymers to protect themselves from unfavorable solvents; and the relationship between the enzyme surface characteristics and the polymer features.

“We found that the enzymes indeed select certain polymer sequences that best cover their surface out of the pool of the polymers,” Trung said. “The random copolymers provide the composition and sequence diversity similar to that in disordered enzymes, which explains why they can efficiently cover numerous enzymes in different size, shape, and surface patterns.”

The study, fueled by a grant from the US Department of Energy and support from the Sherman Fairchild Foundation that enabled the computational work, highlights that this special family of copolymers is an excellent candidate material for synthesizing membraneless organelles — the micron-sized liquid droplets inside cells of living organisms — as well as for stabilizing and delivering enzymes across multiple non-biological media.

“Right now, for instance, researchers in the pharmaceutical industry are trying to match sequences perfectly,” Olvera de la Cruz said. “Our discovery provides guidelines to make the dispersion of enzymes much more cost-effective and efficient.”

Olvera de la Cruz and her colleagues now plan to investigate how the membraneless organelles might spontaneously form with these copolymers-enzymes, how to control their sizes, and how the structural properties of the enzymes might be affected inside the organelles.

“The next step will be exploring the possibilities of concentrating different enzymes together, which is highly promising in advancing their catalytic ability, in creating new chemicals, as well as in processing industrial waste, in an efficient fashion,” Olvera de la Cruz said.

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RESEARCH

Posted: Feb 02, 2018      Publication Link

Kirigami nanofluidic devices


(Nanowerk Spotlight) Recent research in nanofluidics has adopted reconstructed layered two-dimensional (2D) sheets (such as graphene oxide or clay) as a promising material platform for nanofluidics. These membranes contain a high volume fraction of interconnected 2D nanochannels.

This nanochannel fabrication method is straightforward and scalable, and does not rely on lithography or etching.

"Compared to other scalable nanofluidic materials such as anodized aluminum oxide membrane, block copolymer membrane and nanofluidic crystals, a unique feature of such layered membranes is that the channels are horizontally aligned and the channel height (i.e., interlayer spacing), which is responsible for confinement of the electrolyte, remains uniform throughout the entire thin film," Jiaxing Huang, a Professor of Materials Science and Engineering at Northwestern University, tells Nanowerk. "Therefore, nanofluidic ionic transport properties are maintained regardless of the lateral dimensions or shape of the 2D nanochannel network."

The researchers termed this process, which opens up a range of new opportunities for manipulating ionic transport by tailoring the shape of the films, kirigami nanofluidics. They reported their findings in Materials Chemistry Frontiers ("Kirigami nanofluidics").

The work shows that these 2D membranes behave like 'ionic wafers', which can be patterned by kirigami to realize device functions such as diodes.

"Although these ionic functions are still quite simple, compared to electronic devices, they did show that ionic transport through a layered membrane, which is a nanoscale phenomenon, could be tuned by tailor cutting the macroscopic shape of the film," notes Jun Gao, the paper's first author. "We hope the mechanistic understanding and the demonstrations in this work can help people better understand ionic transport through these 2D films, which is useful for designing large scale nanofluidic channels arrays for separation purposes."

Compared to the classical ionic diodes, which typically are made of channels with asymmetric ends such as a conical nanopore (Figure 1a), the 2D nanochannels have uniform channel size (i.e. interlayer spacing) throughout the entire volume of the film (Figure 1b). This simplifies the factors affecting ionic transport, making it possible to control the overall ionic conductance by tailoring the ionic resistance at the channel-reservoir interfaces.

Figure 1: Schematic drawings highlighting the microstructural differences between (a) a conical-shaped nanopore, whose channel size is nonuniform and (b) a GO film that has uniform channel size, despite of asymmetric macroscopic shape. (© RSC)

For example, a graphene oxide film with asymmetric ends, such as a T-shape, exhibits ionic rectification (Figure 2d). While shapes with symmetric ends, such as a diode-sign, exhibits no rectification (Figure 2c).

Figure 2: Kirigami nanofluidic devices. (a) A rectangular piece of GO paper shows symmetric current under both forward and reverse bias. (b) When cut into a trapezoidal shape, the device rectifies the current, exhibiting typical diode-like behavior. (c) A piece of GO paper with the shape of a 'diode sign' does not show rectifying behavior. (d) A T-shaped GO paper shows a diode-like rectifying current. The insets illustrate the top view of the GO papers. For consistency, the left reservoirs of all devices are designated as the source. These results suggest that current rectification is only determined by the relative widths of the two ends, and not by the shape of the GO paper in between. (© RSC)

 

Kirigami nanofluidics allows the fabrication of nanofluidic devices and the control of their performance in a very straightforward way. For example, the ionic current rectification ratio can be adjusted by 'tailor cutting' the geometry of the film, which has been quite difficult in previous works.

Nanofluidic devices are ionic analogs to semiconductor devices. Kirigami-made resistors and diodes can be connected to realize some simple logic functions such as the AND gate and OR gate.

"An electrolyte confined in nanochannels exhibits unusual behaviors owing to strong influences from the channel walls," explains Erik Luijten, a Professor of Materials Science and Engineering at Northwestern University. "When the size of a charged channel is comparable to the Debye length of the electrolyte, co-ions are effectively repelled from the channel and counterions are concentrated, leading to the so called unipolar ionic transport properties with the counterions as the majority charge carrier."

The team first hypothesized that such nanochannels can be readily formed by stacking up 2D sheets, such as graphene oxide. Indeed, they had previously demonstrated that films of graphene oxide or clay sheets contain massive arrays of parallel 2D nanofluidic channels.

In this regard, films of 2D sheets are conceptually analogous to extrinsically doped semiconductors, a material foundation that has enabled the realization of numerous electronic devices and integrated circuits.
In the current work, Huang's team showed that like semiconductor wafers, papers of graphene oxide can also be 'patterned' to realize some analogous functions such as ionic diodes or logic circuits. The patterning is done by cutting the film into various shapes.

In one demonstration, Huang's team showed that programmable rectification ratio can be realized in multi-armed films, by varying the numbers of arms for the source and drain, respectively.

Figure 3. Programming the rectification ratio. (a) Photo showing a cross-shaped GO paper with four branches. One branch is designated as the drain. By varying the number of branches that are connected to the source, the rectification ratio f can be tuned. (b) Current–voltage measurements show that the forward current varies in direct proportion to the number of source branches used. The reverse-voltage resistance is determined mostly by the edge length of the drain end and therefore remains largely unchanged (© RSC)

Going forward, the scientists are interested in creating nanofluidic devices with active gating function, which would allow us to manipulate nanofluidic transport with more freedom.

Monica Olvera de la Cruz, a co-author of the paper and a Professor of Materials Science and Engineering at Northwestern University, concludes that "It will be very exciting to realize some form of gating mechanism to make ionic transistors, and to integrate all of these device elements to achieve a bit more complex logic or even computing functions."

By Michael Berger – Michael is author of two books by the Royal Society of Chemistry: Nano-Society: Pushing the Boundaries of Technology and Nanotechnology: The Future is Tiny. Copyright © Nanowerk


Honors and Awards

Monica Olvera de la Cruz and Chad Mirkin are recognized by Sherman Fairchild Foundation

Northwestern University’s Monica Olvera de la Cruz and Chad A. Mirkin have received significant five-year grants from the Sherman Fairchild Foundation in support of their innovative materials science research.

Olvera de la Cruz, the Lawyer Taylor Professor of Materials Science and Engineering in the McCormick
School of Engineering, will receive $4.5 million to accelerate the discovery of new functions and application of synthetic structures, including hybrid biological and synthetic assemblies. She will focus on structures that mimic and enhance the action of protein membranes and cells to better understand biological functions, with applications in environmental remediation and health care. The project promises to push forward the field of biomimicry, which seeks to solve pressing problems by emulating nature.

Olvera de la Cruz is recognized internationally for her contributions to analyzing, modeling and designing new materials that mimic effective biological processes. She also is a professor of chemical and biological engineering, chemistry, and physics and astronomy and director of the Center for Computation and Theory of Soft Materials.                               

Mirkin, the George B. Rathmann Professor of Chemistry at the Weinberg College
of Arts and Sciences, will receive $5 million to develop a novel design method called “nanocombinatorics.” The chemistry-based approach would systematically and comprehensively screen innumerable nanomaterial combinations and identify the most promising for a given area of study or application.  The resulting encyclopedic resource of high-performance nanomaterials could be used in energy production, environmental remediation, health care, computing technology and homeland security.

Mirkin is world-renowned for his nanoscience expertise and invention of spherical nucleic acids and the development of biological and chemical diagnostic and therapeutic systems based upon them. He also is director of Northwestern’s International Institute for Nanotechnology and a professor of medicine, chemical and biological engineering, biomedical engineering, and materials science and engineering.

The funds raised through We Will. The Campaign for Northwestern are helping realize the transformational vision set forth in Northwestern’s strategic plan and solidify the University’s position among the world’s leading research universities.


RESEARCH

Breaking the Protein-DNA Bond

Study finds that free-floating proteins break up protein-DNA bonds at the single-binding site

Apr 4, 2017 //  Amanda Morris

The verdict is in: too many single, flirty proteins can break up a strong relationship.

A new interdisciplinary Northwestern University study reports that the important protein-DNA bond can be broken by unbound proteins floating around in the cell. This discovery sheds light on how molecules self-organize and how gene expression is dynamically controlled.

“The way proteins interact with DNA determines the biological activity of all living organisms,” said John F. Marko, professor of molecular biosciences, physics, and astronomy in Northwestern’s Weinberg College of Arts and Sciences. “Inevitably, any malfunction in this interaction network can lead to malevolent conditions. It is paramount to precisely understand the interaction mechanisms underlying protein-DNA associations.”

To understand this vital relationship, Marko led a study examining the sites where a single protein binds to DNA. Strands of DNA have specific sites on which other molecules can bind and become a part of the DNA’s genetic code. One type of DNA-binding proteins, called transcription factors (TF), are key players in the transcription of genetic information from DNA to messenger RNA (mRNA) to produce new proteins or other types of RNA. TF proteins control the biological processes in living cells by binding and unbinding to DNA.

In the experiment, Marko and his team developed a concentration of TF proteins bound to DNA mixed with unbound TF proteins, which competed with the bound proteins for their binding sites. They observed that unbound proteins caused the bound proteins to dissociate from the DNA. The unbound proteins then stole the newly available single-binding sites.

“Our experiments show that dissociation happens on the level of a single protein-DNA interaction,” Marko said. “This is new information for the field.”

Monica Olvera de la Cruz

Supported by the National Institutes of Health and National Science Foundation, the research was published online this week in the journal Proceedings of the National Academy of Sciences. Ramsey Kamara, a former postdoctoral researcher in Marko’s laboratory, served as the paper’s first author. Northwestern Engineering’s Monica Olvera de la Cruz, the Lawyer Taylor Professor of Materials Science and Engineering, coauthored the paper.

Olvera de la Cruz led the development of a theoretical model and performed molecular dynamics simulations to show the prevalence of the protein-DNA break up at the single-binding site due to the competitor proteins. This disproves former beliefs that protein-DNA bonds were unaffected by unbound proteins and instead resulted from more “cooperative” interactions among many molecules, large protein clusters, or long DNA segments.

“Our results suggest that protein-DNA dissociation could have a profound effect on the dynamics of biological processes that depend on protein binding in vivo,” Olvera de la Cruz said. “This may be an important factor to take into account when modeling gene expression in living cells.”


Olvera de la Cruz to Receive 2017 APS Polymer Physics Prize

The prestigious award honors her contributions to the theoretical understanding of polymers

Northwestern Engineering’s Monica Olvera de la Cruz to receive the 2017 Polymer Physics Prize from the American Physical Society (APS).

Olvera de la Cruz was selected for her “outstanding contributions to the theoretical understanding of polymers and the effects of electrostatic interactions on their structure and properties.” She will officially accept the award at the APS March Meeting next year.


“I am honored to receive the 2017 APS Polymer Physics Prize,” said Olvera de la Cruz, the Lawyer Taylor Professor of Materials Science and Engineering in Northwestern’s McCormick School of Engineering. “It is given to highly distinguished scientists, including three Nobel Prize winners — Pierre Gilles de Gennes, Peter J.W. Debye, and Paul Flory — and my PhD adviser Sir Sam Edwards.”

Olvera de la Cruz’s research focuses on the development of models to describe the self-assembly of heterogeneous molecules, including amphiphiles, copolymers, and synthetic and biological polyelectrolytes. She also studies the segregation and interface adsorption in multicomponent complex fluids. Her group’s work has resulted in a revised model of ionic-driven assembly, and its investigations into soft and condensed matter physics have advanced scientific knowledge and opened new research fields of technological importance.

“Polymers have fascinating physical properties,” Olvera de la Cruz said. “They have attracted studies by scientists and mathematicians for decades, given that they are one-dimensional molecules with nanoscale dimensions that are capable of taking multiple conformations.”

A member of the National Academy of Sciences, Olvera de la Cruz has received several other honors and awards, including the Engineering and Applied Sciences Cozzarelli Prize from the National Academies, a National Security Science and Engineering Faculty Fellowship, an Alfred P. Sloan Fellowship, and the NSF Presidential Young Investigator Award and the David and Lucile Packard Fellowship in Science and Engineering. She is also a fellow of the American Academy of Arts and Sciences and the American Physical Society.


Honors and Awards

CHAD MIRKIN HONORED AT AWARDS CEREMONY IN ISRAEL

Northwestern’s Chad Mirkin (center) accepts the 2016 Dan David Prize in the Future Time Dimension from Joseph Klafter (left), president of Tel Aviv University and chairman of the Dan David Prize Board of Directors. Northwestern President Morton Schapiro (right), along with other Northwestern officials, also attended the May 22 awards ceremony. Photo by Hadari Photography