Scientists take key step toward custom-made nanoscale chemical factories

Researchers create new function in tiny protein shell structures----- Scientists have for the first time reengineered a building block of a geometric nanocompartment that occurs naturally in bacteria. They introduced a metal binding site to its shell that will allow electrons to be transferred to and from the compartment. This provides an entirely new functionality, greatly expanding the potential of nanocompartments to serve as custom-made chemical factories.[F1] Scientists hope to tailor this new use to produce high-value chemical products, such as medicines, on demand.[F2]  The sturdy nanocompartments, which are polyhedral shells composed of triangle-shaped sides and resemble 20-sided dice, are formed by hundreds of copies of just three different types of proteins. Their natural counterparts, known as bacterial microcompartments or BMCs, encase a wide variety of enzymes that carry out highly specialized chemistry in bacteria.--Researchers at the Department of Energy's Lawrence Berkeley National Laboratory (Berkeley Lab) devised synthetic shell structures derived from those found in a rod-shaped, ocean-dwelling bacterium, Haliangium ochraceum, and reengineered one of the shell proteins to serve as a scaffold for an iron-sulfur cluster found in many forms of life. The cluster is known as a "cofactor" because it can serve as a helper molecule in biochemical reactions.--BMC-based shells are tiny, durable and naturally self-assemble and self-repair, which makes them better-suited for a range of applications than completely synthetic nanostructures.--"This is the first time anyone has introduced functionality into a shell.[F3]  We thought the most important functionality to introduce was the ability to transfer electrons into or out of the shell," said Cheryl Kerfeld, a structural biologist at Berkeley Lab and corresponding author in this study. Kerfeld's research group focuses on BMCs. Kerfeld holds joint appointments with Berkeley Lab's Molecular Biophysics and Integrated Bioimaging (MBIB) Division, UC Berkeley and the MSU-DOE Plant Research Laboratory at Michigan State University (MSU). "That greatly enhances the versatility of the types of chemistries you can encapsulate in the shell and the spectrum of products to be produced," she said. "Typically, the shells are thought of as simply passive barriers."[F4] Researchers used X-rays at Berkeley Lab's Advanced Light Source (ALS) to show, in 3-D and at the atomic scale, how the introduced iron-sulfur cluster binds to the engineered protein. The study is now online in the Journal of the American Chemical Society.Enzymes inside natural BMCs can convert carbon dioxide into organic compounds that can be used by the bacteria, isolate toxic or volatile compounds from the surrounding cell, and carry out other chemical reactions that provide energy for the cell. In this study, researchers introduced the iron-sulfur cluster into the tiny pores in the shell building block. This engineered protein serves as an electron relay across the shell, which is key to controlling the chemical reactivity of substances inside the shell. Clement Aussignargues, the lead author of the study and postdoctoral researcher in the MSU-DOE Plant Research Laboratory in Michigan, said, "The beauty of our system is that we now have all the tools, notably the crystallographic structure of the engineered protein, to modify the redox potential of the system--its ability to take in electrons (reduction) or give off electrons (oxidation).-"If we can control this, we can expand the range of chemical reactions we can encapsulate in the shell. The limit of these applications will be what we put inside the shells, not the shells themselves."[F5] He added, "Creating a new microcompartment from scratch would be very, very complicated. That's why we're taking what nature put before us and trying to add to what nature can do." To design the metal binding site, Kerfeld's group first had to solve the structures of the building blocks of the nanocompartment to use as the template for design. These building blocks self-assemble into synthetic shells, which measure just 40 nanometers, or billionths of a meter, in diameter. The natural form of the shells can be up to 12 times larger. The iron-sulfur cofactor of the engineered protein, which was produced in E. coli bacteria, was very stable even when put through several redox cycles--a characteristic essential for future applications, Aussignargues said. "The engineered protein was also more stable than its natural counterpart, which was a big surprise," he said. "You can treat it with things that normally make proteins fall apart and unwind."[F6]   A major challenge in the study was to prepare the engineered protein in an oxygen-free environment to form tiny crystals that best preserve their structure and their cofactor for X-ray imaging, Kerfeld said. The crystals were prepared in an air-sealed glovebox at MSU, frozen, and then shipped out for X-ray studies at Berkeley Lab's ALS and SLAC National Accelerator Laboratory's Stanford Synchrotron Radiation Lightsource (SSRL). In follow-up work, the research team is exploring how to incorporate different metal centers into BMC shells to access a different range of chemical reactivity[F7] , she said. "I'm working on incorporating a completely different metal center, which has a very positive reduction potential compared to the iron-sulfur cluster," said Jeff Plegaria, a postdoctoral researcher at the MSU-DOE Plant Research Laboratory who contributed to the latest study. "But it is the same sort of idea: To drive electrons in or out of the compartment." He added, "The next step is to encapsulate proteins that can accept electrons into the shells, and to use that as a probe to watch the electron transfer from the outside of the compartment to the inside." That will bring researchers closer to creating specific types of pharmaceuticals or other chemicals-- Other scientists involved in the study were from MSU, The Pennsylvania State University and Brooklyn College. The work was supported by the U.S. DOE Office of Science, MSU AgBio Research and the European Union's PEPDIODE project. The ALS and SLAC's SSRL are both DOE Office of Science User Facilities.-Story Source-The above post is reprinted from materials provided by DOE/Lawrence Berkeley National Laboratory. The original item was written by Glenn Roberts Jr.. Journal Reference-Clément Aussignargues, Maria-Eirini Pandelia, Markus Sutter, Jefferson S. Plegaria, Jan Zarzycki, Aiko Turmo, Jingcheng Huang, Daniel C. Ducat, Eric L. Hegg, Brian R. Gibney, Cheryl A. Kerfeld. Structure and Function of a Bacterial Microcompartment Shell Protein Engineered to Bind a [4Fe-4S] Cluster. Journal of the American Chemical Society, 2016; DOI: 10.1021/jacs.5b11734  DOE/Lawrence Berkeley National Laboratory. "Scientists take key step toward custom-made nanoscale chemical factories: Researchers create new function in tiny protein shell structures." ScienceDaily. ScienceDaily, 4 February 2016. <>.

 [F1]Implications here is that you can use this as a function of a bacterium or even viral to introduce and manufacture whatever you program into the compartments~ anything from a biological agent to a technical device interface with any type of processor

 [F2]I find this hilarious-this would be more to the truth of BW agents and for military use or and R&D the “medicines “would be  more like agents being delivered into whatever they wish to cause or shutdown or manufacture whatever is in the program

 [F3]Another way of expressing this “first time introducing a program or commands into a shell’

BASCIALLY controlling the process of the bacteria and to make more of what ever you wish with the capacity to self assemble and to repair which would make this challenging to get under control~due to the capacity to follow a program would also indicate that it is able to have the program over written this would imply very strongly that environmental factors could as well cause this to mutate the program set up

 [F4]Consider the implications in vaccines ~ a self assembling of a carrier with different components incorporated in the polyhedral shells entering int the blood steram attaching itself to the cellular matrix bypassing the myelin and entering the mitochondria and overwriting the gene code and the DNA functions and releasing a plethora of programming into the host ~ this would be a epidemic like effect and a disarming of the immune system or central nervous system or the skeletal system or any other are you could overwhelm

 [F5]Many natural biological systems—such as biofilms, shells and skeletal tissues—are able to assemble multifunctional and environmentally responsive multiscale assemblies of living and non-living components. By using inducible genetic(Genetics. to increase expression of (a gene) by inactivating a negative control system or activating a positive control system; Biochemistry. to stimulate the synthesis of (a protein, especially an enzyme) by increasing gene transcription.  ) circuits and cellular communication circuits to regulate Escherichia coli curli amyloid production, we show that E. coli cells can organize self-assembling amyloid fibrils across multiple length scales, producing amyloid-based materials that are either externally controllable or undergo autonomous patterning. We also interfaced curli fibrils with inorganic materials, such as gold nanoparticles (AuNPs) and quantum dots (QDs), and used these capabilities to create an environmentally responsive biofilm-based electrical switch, produce gold nanowires and nanorods, co-localize AuNPs with CdTe/CdS QDs to modulate QD fluorescence lifetimes, and nucleate the formation of fluorescent ZnS QDs. This work lays a foundation for synthesizing, patterning, and controlling functional composite materials with engineered cells

 [F6]This should make one think if we are now utilizing what is natural in design and adding to it and increasing the fortification factor of the genome then what you are getting here is something in a form of augmentation-enhancements or a dangerious mutation which in any case is affecting the evolution of the construct

 [F7]Synthetic Analog Computation in Living Cells.

A central goal of synthetic biology is to achieve multi-signal integration and processing in living cells for diagnostic, therapeutic and biotechnology applications1. Digital logic has been used to build small-scale circuits, but other frameworks may be needed for efficient computation in the resource-limited environments of cells. Here we demonstrate that synthetic analog gene circuits can be engineered to execute sophisticated computational functions in living cells using just three transcription factors. Such synthetic analog gene circuits exploit feedback to implement logarithmically linear sensing, addition, ratiometric and power-law computations. The circuits exhibit Weber’s law behaviour as in natural biological systems, operate over a wide dynamic range of up to four orders of magnitude and can be designed to have tunable transfer functions. Our circuits can be composed to implement higher-order functions that are well described by both intricate biochemical models and simple mathematical functions. By exploiting analog building-block functions that are already naturally present in cells, this approach efficiently implements arithmetic operations and complex functions in the logarithmic domain. Such circuits may lead to new applica- tions for synthetic biology and biotechnology that require complex computations with limited parts, need wide-dynamic-range biosen- sing or would benefit from the fine control of gene expression. [Nature 2013]