Every once in a great while a piece of very interesting science comes along, quietly, until more and more people notice that not only is important but it may be right. Then scientists get into high gear and start doing more intensive experimenting. Sometimes the science press or even the popular media catch wind of it and the hype begins. Eventually, I should say usually, something more definitive can be said about it. In some cases, like the noisy introduction of “cold fusion,” it becomes a terrible bust very quickly. In other cases, like some of Einstein’s work, it took several contentious decades.
I’m setting the stage for one of those quiet pieces of very interesting science. It’s about proteins. Proteins are the building blocks of life. The genetic code in DNA provides the template to manufacture protein into all the cells of an organism. So we’re talking about something fundamental to life as we know it.
Proteins are made by stringing together amino acids. For general purposes there are twenty amino acids in protein and they can be put together in endless combinations, some in short chains (yeast averages 466 amino acids), some long chains (titins have nearly 27,000 amino acids) and everything in-between. The pattern of amino acids determines much of the functionality of the protein. But that’s not all. Proteins also have shape – threads, coils, curves, bends – they are folded. The folding of proteins is just as important to the functionality as the sequence of amino acids. A simple analogy would be fitting together the pieces of a puzzle; only pieces cut a certain way fit into other pieces until finally the whole puzzle can be assembled. To extend the analogy: Proteins are three-dimensional puzzle pieces. They are generally very complicated in shape. Even a small protein of only 100 amino acids can theoretically have 10^100 (ten to the hundredth power) different configurations.
In this bewildering number of possible configuration are some of the great mysteries in biology. How are the configurations of proteins determined, and what makes them fold? With all the possible configurations and the complexity of so many proteins, it should take some time for a protein to take on a final configuration. Yet it is known that most protein reconfigurations occur in nanoseconds; how does this work?
The study of how proteins are manufactured and folded into correct shapes is a vast field of study (loosely called proteomics). In this case, the research by two Mongolian scientists, Liaofu Luo at the Inner Mongolia University and Jun Lu at the Inner Mongolia University of Technology (both in Hohhot, China) and published in arXiv, 18 February 2011, Temperature Dependence of Protein Folding Deduced from Quantum Transition, deals with the problem of how proteins change their configurations almost instantaneously.
As scientists usually do, Luo and Lu started with the research already done. (It’s called “scanning the literature.”) They noticed a particular area of protein behavior that was a real problem to explain. In most chemistry, organic chemistry included, the application of heat increases the speed of reaction. This is called the Arrhenius principle. In research on proteins, it was assumed (given their chemical composition) proteins would uniformly fold as they cool down and unfold as they heat up. (Think of a balloon expanding and shrinking with the temperature of the air inside.) The experiments didn’t bear this out; the rate of folding or unfolding according to temperature change was unequal (asymmetric) and uneven (nonlinear). To try to explain this in a traditional manner, scientists referred, for example, to the way parts of a protein that repel or attract water could react very quickly. Some of these explanations seem to work for particular or limited types of protein configurations, but none of the proposed explanations – which Luo and Lu refer to as ‘classical mechanics’ – fit protein transformation in general.
It seemed obvious to them (and may soon to others) that quantum mechanics could provide a better explanation, or in science-speak – a better fit to the observed data. An important argument in favor of a quantum analysis occurred to them: In recent biochemistry a great deal of work is done with ‘tagging’ or ‘marking’ molecules with fluorescent and phosphorescent materials. It’s well known that fluorescence and phosphorescence are phenomena closely related to protein folding and they can only be understood in terms of quantum transition between molecules. Why shouldn’t protein folding also fit within the framework of quantum theory?
Luo and Lu then set about to demonstrate this relationship through mathematics. What they discovered is something like this: In classical mechanics the transition of a protein molecule from one configuration to another should proceed in a series of steps (transition states), adding time at each step – meaning it should be relatively slow. With a quantum transition, the protein could change configuration by ‘jumping’ – skipping all the transition steps – to the final configuration. They call this quantum folding and they developed a mathematical model that shows how the folding, which is virtually instantaneous, would react to change in temperature.
For verification of what the math was showing them, they used the model with the results of real world experimental data. Their quantum transition model matched the folding curves for 15 different proteins and also provides an explanation for the different rates of folding and unfolding among these proteins.
In short, it looks like their model may work for many, if not all, protein folding. Some reports are jumping the gun and calling this the “first universal law of protein folding.” It’s way too early for that.
Luo and Lu’s paper is short, a mere 16 pdf pages, and the model is unpretentious mathematically. (Luo has several other related papers on arXiv.) It comes from unknown researchers in an unknown corner of the academic world, and it’s published on the open-source arXiv system. The lack of pedigree means that it will take more time than usual for scientists around the world to learn of it, examine it, and possibly test it. So it will be interesting to see what – if any – the reactions will be, and whether the research constitutes real breakthrough or something less.
In any case, their work joins the growing list of research that links quantum phenomena to biological processes. If it holds up (their research, and quantum biology as whole) it’s like discovering a brave new world of complexity in the realm of biology.