Tag Archives: biomolecules

Similarities between biological molecules and synthetic nanocrystals extend beyond size

Researchers at the University of Illinois at Urbana-Champaign have determined that there are more similarities between biological molecules and synthetic nanocrystals than formerly believed, according to a Dec. 17, 2013 news item on Nanowerk (Note: A link has been removed),

Researchers have long thought that biological molecules and synthetic nanocrystals were similar only in size. Now, University of Illinois at Urbana-Champaign chemists have found that they can add reactivity to the list of shared traits. Atoms in a nanocrystal can cooperate with each other to facilitate binding or switching, a phenomenon widely found in biological molecules.

The finding could catalyze manufacturing of nanocrystals for smart sensors, solar cells, tiny transistors for optical computers, and medical imaging. Led by chemistry professor Prashant Jain, the team published its findings in the journal Nature Communications (“Co-operativity in a nanocrystalline solid-state transition”).

A Dec. 16, 2013 University of Illinois at Urbana-Champaign news release, which originated the news item, explains why the scientists are so interested and how they went about their investigation,

“In geological, industrial and domestic environments, the nanoscale grains of any material undergo chemical transitions when they are put under reactive conditions,” Jain said. “Iron rusting over time and diamond forming from carbon are examples of two commonly occurring transitions. Understanding how these transitions occur on the scale of the tiniest grains of the material is a major motivation of our work.”

Scientists can exploit such transitions to make nanocrystals that conform to a particular structure. They can make a nanocrystal of one material and transform it into another material, essentially using the original nanocrystal framework as a template for creating a nanocrystal of the new material with the same size and shape. This lets researchers create nanocrystals of new materials in shapes and structures they may not be able to otherwise.

In the new study, the researchers transformed tiny crystals of the material cadmium selenide to crystals of copper selenide. Copper selenide nanocrystals have a number of interesting properties that can be used for solar energy harvesting, optical computing and laser surgery. Transformation from cadmium selenide creates nanocrystals with a purity difficult to attain from other methods.

The researchers, including graduate student Sarah White, used advanced microscopy and spectroscopy techniques to determine the dynamics of the atoms within the crystals during the transformation and found that the transformation occurs not as a slow diffusion process, but as a rapid switching thanks to co-operativity.

The researchers saw that once the cadmium-selenide nanocrystal has taken up a few initial copper “seed” impurities, atoms in the rest of the lattice can cooperate to rapidly swap out the rest of the cadmium for copper. Jain compares the crystals to hemoglobin, the molecule in red blood cells that carries oxygen. Once one oxygen molecule has bound to hemoglobin, other binding sites within hemoglobin slightly change conformation to more easily pick up more oxygen. He posits that similarly, copper impurities might cause a structural change in the nanocrystal, making it easier for more copper ions to infiltrate the nanocrystal in a rapid cascade.

The researchers reproduced the experiment with silver, in addition to copper, and saw similar, though slightly less speedy, cooperative behavior.

Now, Jain’s team is using its advanced imaging to watch transitions happen in single nanocrystals, in real time.

“We have a sophisticated optical microscope in our lab, which has now allowed us to catch a single nanocrystal in the act of making a transition,” Jain said. “This is allowing us to learn hidden details about how the transition actually proceeds. We are also learning how one nanocrystal behaves differently from another.”

Next, the researchers plan to explore biomolecule-like cooperative phenomena in other solid-state materials and processes. For example, co-operativity in catalytic processes could have major implications for solar energy or manufacturing of expensive specialty chemicals.

“In the long term, we are interested in exploiting the co-operative behavior to design artificial smart materials that respond in a switch-like manner like hemoglobin in our body does,” Jain said.

Here’s an image of the various forms of cadmium selenide used in research,

Nanocrystals of cadmium selenide, known for their brilliant luminescence, display intriguing chemical behavior resulting from positive cooperation between atoms, a behavior akin to that found in biomolecules.  Photo courtesy Prashant Jain

Nanocrystals of cadmium selenide, known for their brilliant luminescence, display intriguing chemical behavior resulting from positive cooperation between atoms, a behavior akin to that found in biomolecules. Photo courtesy
Prashant Jain

For the curious, here’s a link to and a citation for the paper,

Co-operativity in a nanocrystalline solid-state transition by Sarah L. White, Jeremy G. Smith, Mayank Behl, & Prashant K. Jain Nature Communications 4, Article number: 2933 doi:10.1038/ncomms3933 Published 12 December 2013

This article is behind a paywall.

Watching zinc, iron, and copper molecules real-time as they interact with biomolecules

Eventually they’re hoping this work will lead to insights about diabetes and cancer. In the meantime, researchers at RIKEN Center for Life Science Technologies (Japan) have developed a new imaging technique that allows them to observe metal molecules interacting with biomolecules in real-time. From the May 2, 2013 news release on EurekAlert,

Metal elements and molecules interact in the body but visualizing them together has always been a challenge. Researchers from the RIKEN Center for Life Science Technologies in Japan have developed a new molecular imaging technology that enables them to visualize bio-metals and bio-molecules simultaneously in a live mouse. This new technology will enable researchers to study the complex interactions between metal elements and molecules in living organisms.

It’s well known we need zinc, iron, and copper in our bodies for proper functioning. Until now, no one has been able to observe the interaction in real-time, from the RIKEN May 2, 2013 press release (which originated the EurekAlert news release),

In the study, the researchers were able to visualise two radioactive agents injected in a tumor-bearing mouse, as well as an anti-tumor antibody labelled with a PET molecular probe agent, simultaneously in the live mouse.

This new revolutionary technology is expected to offer new insights into the relationships between bio-metal elements and associated bio-molecules, and the roles they play in diseases such as diabetes and cancer.

The researchers had to create a camera capable of visualizing the interactions (from the RIKEN press release),

Dr. Shuichi Enomoto, Dr. Shinji Motomura and colleagues, from the RIKEN Center for Life Science Technologies have developed a gamma-ray imaging camera enabling them to detect the gamma-rays emitted by multiple bio-metal elements in the body and study their behavior.

Their second prototype of the system, called GREI–II and presented today in the Journal of Analytical Atomic Spectrometry, enables them to visualize multiple bio-metal elements more than 10 times faster than before, and to do so simultaneously with positron emission tomography (PET).

You can find the research study here.

For those unfamiliar with RIKEN, here’s more from their About RIKEN page,

RIKEN is Japan’s largest comprehensive research institution renowned for high-quality research in a diverse range of scientific disciplines. Founded in 1917 as a private research foundation in Tokyo, RIKEN has grown rapidly in size and scope, today encompassing a network of world-class research centers and institutes across Japan.

Making movies of biomolecules

’tis the season for recycling news; this research about making biomolecular movies was published in Nature Protocols in June 2012 according to the Jan. 4, 2013 news item on phys.org (Note: Links have been removed),

Toshio Ando and co-workers at Kanazawa University [Japan] have developed and used HS-AFM [high-speed atomic force microscopy] to increase our understanding of several protein systems through microscopic movies of unprecedented spatial and temporal resolution. The team have now published a guide to video recording these important cell components, so that other researchers can benefit from this unique technology.

To produce an image, HS-AFM acquires information on sample height at many points by tapping the sample with the sharp tip of a tiny cantilever. Depending on the application, this might involve recording the amplitude and phase of oscillations, or the resonant frequency of the cantilever.

Ando and co-workers use very small cantilevers that afford 10 to 20 times the sensitivity of larger, conventional cantilevers. Copies of their home-made apparatus are now commercially available through the manufacturer Research Institute of Biomolecule Metrology Co., Ltd. (RIBM) in Tsukuba, and record images at least ten times more quickly than their competitors.

There are more details in the news item or for those who want to read the guide, here’s a citation and a link,

Guide to video recording of structure dynamics and dynamic processes of proteins by high-speed atomic force microscopy by Takayuki Uchihashi, Noriyuki Kodera, & Toshio Ando in Nature Protocols 7 (6), 1193–1206 (2012) doi:10.1038/nprot.2012.047

This article is behind a paywall.

Lastly, should anyone wish to purchase the apparatus developed at Kanazawa University from the Research Institute of Biomolecule Metrology Co., Ltd., here’s more about it from the company’s home page,

Dynamic Visualization of nano-scale world

HS-AFM*1.0 – Ando model – is the High-Speed Atomic Force Microscope which was developed based on the research achievements accomplished by Prof. Ando in Kanazawa University. This is the world’s first instrument that broke through the weak point of conventional AFM “low-speed”, and realized the video rate scan. The high-speed scan enables us to capture swinging molecules in solution clearly without blurring. Consequently, the strong anchoring of a sample to the substrate is unnecessary and a dynamic observation is achieved without losing the activities of soft biomolecules.

Protein cages, viruses, and nanoparticles

The Dec. 19, 2012 news release on EurekAlert about a study published by researchers at Aalto University (Finland) describes a project where virus particles are combined with nanoparticles to create new metamaterials,

Scientists from Aalto University, Finland, have succeeded in organising virus particles, protein cages and nanoparticles into crystalline materials. These nanomaterials studied by the Finnish research group are important for applications in sensing, optics, electronics and drug delivery.

… biohybrid superlattices of nanoparticles and proteins would allow the best features of both particle types to be combined. They would comprise the versatility of synthetic nanoparticles and the highly controlled assembly properties of biomolecules.

The gold nanoparticles and viruses adopt a special kind of crystal structure. It does not correspond to any known atomic or molecular crystal structure and it has previously not been observed with nano-sized particles.

Virus particles – the old foes of mankind – can do much more than infect living organisms. Evolution has rendered them with the capability of highly controlled self-assembly properties. Ultimately, by utilising their building blocks we can bring multiple functions to hybrid materials that consist of both living and synthetic matter, Kostiainen [Mauri A. Kostiainen, postdoctoral researcher] trusts.

The article which has been published in Nature Nanotechnology is free,

Electrostatic assembly of binary nanoparticle superlattices using protein cages by Mauri A. Kostiainen, Panu Hiekkataipale, Ari Laiho, Vincent Lemieux, Jani Seitsonen, Janne Ruokolainen & Pierpaolo Ceci in Nature Nanotechnology (2012) doi:10.1038/nnano.2012.220  Published online 16 December 2012

There’s a video demonstrating the assembly,

From the YouTube page, here’s a description of what the video is demonstrating,

Aalto University-led research group shows that CCMV virus or ferritin protein cages can be used to guide the assembly of RNA molecules or iron oxide nanoparticles into three-dimensional binary superlattices. The lattices are formed through tuneable electrostatic interactions with charged gold nanoparticles.

Bravo and thank  you to  Kostiainen who seems to have written the news release and prepared all of the additional materials (image and video). There are university press offices that could take lessons from Kostiainen’s efforts to communicate about the work.

Environment influences nanomaterial reactions to biological cells

The discussion I’ve seen around nanomaterials and toxicological effects has largely centered on shapes, size, aggregate/agglomerate, etc. By contrast, Carl Walkey’s July 24, 2012 Nanowerk Spotlight essay focuses on nanomaterial surfaces, bare or coated with serum proteins (Note: I have removed links),

Biomolecule adsorption to nanomaterials is usually studied from physiological fluids with suspended biomolecules. Examples include blood serum/plasma, pulmonary surfactant, and synovial fluid. However, until now the amount of those molecules has not been considered relevant to the study. In a recent article appearing in ACS Nano (“Effects of the Presence or Absence of a Protein Corona on Silica Nanoparticle Uptake and Impact on Cells”), Drs. Anna Salvati, Kenneth Dawson, and their colleagues at the University College in Dublin, Ireland, show that if nanoparticles are exposed directly to cells in the absence of suspended biomolecules, the nanoparticles will extract biomolecules directly from cells themselves.

In their experiments, the team exposed silica nanoparticles to cells in two sets. One set was introduced into cell culture media that was supplemented with the usual concentration of fetal bovine serum, and the other into media that had no serum additives. They then incubated both sets of particles with a lung cancer cell line and measured particle uptake kinetics and cell adhesion. Nanoparticles treated under both conditions associated with cells. However, the particles that were incubated in media alone associated to a much greater extent than those that were first incubated in serum. This indicates that the affinity of the bare nanoparticle surface to the cell is much higher than the affinity of an equivalent surface that is coated with serum proteins. [emphasis mine] Similar observations are reported before for other systems, where it was also found that uptake under serum-free conditions is higher.

Moe specifically,

“When the nanomaterial is put in contact with a physiological environment, it is given a menu of possible biomolecules to adsorb” explains Dawson. “It will essentially go shopping for the biomolecules that it wants. Over time, it will exchange with the environment until it finds the things that it really likes most. If you don’t give it enough biomolecules in the form of serum, it will extract components from the cells themselves.”

The same silica nanoparticles exposed to cells in the two different conditions had different cellular responses as well. Most of the serum-coated particles were taken up within vesicles in the cell cytoplasm and produced no overt signs of toxicity. In contrast, the particles without a serum coating adhered to the cell surface to a greater extent, were present in vesicles, and some were also found free-floating in the cytoplasm. Exposure to particles in absence of serum significantly decreased cell viability and caused cells to take on a rounded morphology that is indicative of cell death. Dawson believes that cell death from uncoated particles is the result of strong interactions between the particle surface and the cell surface, which may damage the cell membrane, and/or initiate aberrant signaling cascades. When serum proteins are adsorbed to the nanoparticles, they ‘passivate’ the surface and limit direct nanomaterial-cell interactions.

When considering the early interactions of a nanomaterial with a cell, Dawson points out that one cannot think of the nanomaterial alone. Instead, one must think of the nanoparticle and its adsorbed biomolecules as a fundamental unit. [emphasis mine]

Most importantly,

Dawson believes that researchers must pay closer attention to the composition of the biomolecular environment surrounding the particles and cells when performing in vitro experiments. In other words, it is as important to consider the composition of the biomolecules in the media as it is to consider the chemical nature of the nanoparticle and the cell type. [emphasis mine]

“What’s absolutely clear is that depending on the type of dispersion that you make up, whether you add 10% serum or 20% serum, you get different levels of cell uptake” says Dawson. “Indeed, you get different levels of damage as well. It is therefore not meaningful to say that the nanoparticle is or is not toxic in that simplistic way. You can make a material toxic if you really want to make it toxic. You can make many materials damage cells simply because these have high surface energy. However, in a realistic physiological environment, part of the particle surface is covered and so that kind of damage would not be applicable.”

I encourage anyone who’s interested in nanotoxicology to read Walkey’s essay in full as I’ve excerpted only a portion.

BTW, Carl Walkey is a PhD graduate student at the University of Toronto and a member of the Integrated Nanotechnology & Biomedical Sciences Laboratory (INBS). I last mentioned Walkey in my July 12, 2012 posting about his Nanowerk Spotlight essay on nanotoxicology and animal studies.