Tag Archives: elastomeric proteins

Cells and transistors

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Analog/digital, is there a difference? After reading the latest from MIT’s (Massachusetts Institute of Technology) Research Laboratory Electronics (RLE), the answer turns out to be no, when it comes to transistors. From the Sept. 29, 2011 news item on Nanowerk,

A transistor is basically a switch: When it’s on, it conducts electricity; when it’s off, it doesn’t. [emphases mine] In a computer chip, those two states represent 0s and 1s.

But in moving between its nonconductive and conductive states, a transistor passes through every state in between — slightly conductive, moderately conductive, fairly conductive — just as a car accelerating from zero to 60 passes through every speed in between. Because the transistors in a computer chip are intended to perform binary logic operations, they’re designed to make those transitional states undetectable. [emphases mine]

The MIT researchers will be discussing their work using analog transistors to increase the concentrations of two different proteins in cells. From the news item on Nanowerk,

At the Biomedical Circuits and Systems Conference in San Diego in November, Sarpeshkar [Rahul Sarpeshkar, associate professor of electrical engineering], research scientist Lorenzo Turicchia, postdoc Ramiz Daniel and graduate student Sung Sik Woo, all of RLE, will present a paper in which they use analog electronic circuits to model two different types of interactions between proteins and DNA in the cell. The circuits mimic the behaviors of the cell with remarkable accuracy, but perhaps more important, they do it with far fewer transistors than a digital model would require.

Here’s a graphic representation of transistors in a cell (downloaded from the MIT News Office page for this research,

Graphic: Christine Daniloff

This works seems to be signaling (pun noted) a change in how systems biology and synthetic biology researchers think about biological systems. From the Sept. 28, 2011 news item by Larry Hardesty for the MIT News Office,

Since the completion of the Human Genome Project, two thriving new disciplines — synthetic biology and systems biology — have emerged from the observation that in some ways, the sequences of chemical reactions that lead to protein production in cells are a lot like electronic circuits. In general, researchers in both fields tend to analyze reactions in terms of binary oppositions: If a chemical is present, one thing happens; if the chemical is absent, a different thing happens.

But Rahul Sarpeshkar, an associate professor of electrical engineering in MIT’s Research Laboratory of Electronics (RLE), thinks that’s the wrong approach. “The signals in cells are not ones or zeroes,” Sarpeshkar says. “That’s an overly simplified abstraction that is kind of a first, crude, useful approximation for what cells do. But everybody knows that’s really wrong.”

From what I understand of the synthetic biology and systems biology communities, this is a major change.

Nano, proteins, and Dr. Hongbin Li: part 1

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Here’s the interview I mentioned a few days ago. I now have the answers to some questions I sent Dr. Hongbin Li (University of British Columbia) about the work he recently had published in Nature Nanotechnology (June 29, 2008 online edition). (Note: I don’t usually give links to articles behind paywalls as a lot of people won’t have access.)

Short version: Dr. Li and his team have taken a protein G and attached the fragment of an antibody to one of the protein’s binding sites with the consequence that the protein can act as either a spring or a shock absorber. They’re calling it a ‘chameleon’ nanomaterial. You can read more about it here at UBC Science or here at Nanowerk.

Dr. Li kindly took the time to answer my questions before he leaves for China this Thursday (July 10, 2008). I don’t understand the details of Dr. Li’s work very well and so my questions were largely for clarification. He’s working with a  protein G and I’ve come across G proteins in some literature research I was doing on morphine, and opioid receptors. So, my first question and Dr. Li’s response was  this:

  1. There is a super family of G proteins made up of many subsets. You have used one of these G proteins adhering an antibody fragment at one of its receptor sites. Is this more or less correct?

Response: the protein GB1 we are using has nothing to do with G proteins! GB1 is from protein G, which is a bacterial surface protein and its biological function is not known. Protein G has been widely used for purifying IgG antibodies.

I shouldn’t be surprised to find out that somebody thought it would a good idea to give two different proteins identical names simply reversing the order in which the qualifier is applied with the consequence that there’s a G protein and a protein G  They do that in French where some adjectives change their meaning based on the placement either before or after the noun (but I digress).

The next question had to do with the antibody:

  1. Is an antibody fragment what it sounds like? (i.e. It’s an antibody that’s been sliced up and you are using a fragment.)

Response: IgG antibody can be digested into fragments by proteases. For example, IgG antibody can be digested into Fc fragment and Fab fragment. We used Fc fragment in our study.

I was thinking that the antibody was being broken into fragments by some sort of mechanical process but this sounds like a biological process.

My final question in today’s posting:

  1. I’ve seen the terms ‘synthetic protein’ and ‘mutant protein’ in the various articles about your work. Do you have a preference for one of these terms over the other? And why?

Response: depending on different context, our engineered protein can be called as either synthetic protein or mutant protein. Mutant protein refers to the fact that GT18P and GV54P are mutants of GB1.

Part 2 tomorrow and thank you Dr. Hongbin Li.