Don’t Neglect Protein QC
Protein samples need – and deserve – special treatment, if you expect the best results from your experiments.
We hear it all too often: the study of biological systems is becoming increasingly complex. However, I’d like to ask, is it also becoming quantitative? Not in the sense of measuring more and more parameters, but in measuring basic parameters with an increased level of precision? Sadly, this is probably not the case.
From my own experience and that of my colleagues working in protein binding biotechnology, it is clear that little consideration is given to the handling of proteins in both academia and industry. A red warning light should be flashing for anyone needing to rely on quantitative, experimental data!
The evidence suggests that, all too often, even simple rules in protein preparation have been forgotten or, even worse, ignored due to limited time or resources. Scientists think that they can get away with not implementing even basic quality control when handling proteins. Nevertheless, proteins are special and need special care to yield solid and reliable results.
For example, proteins are obtained from other laboratories or bought directly from suppliers. And, without even checking them internally, it is assumed that the proteins “should work”. But, sometimes a very small change of buffer conditions lead to agglomeration or dysfunctional, unfolded states. A couple of simple questions need answering: did I really check the robustness of the buffer system? Does the melting temperature or circular dichroism of the protein indicate that it is in a well-defined folded state?
Everybody knows that checking the effects of freezing and thawing on protein samples is cumbersome, but it is necessary to guarantee the reproducibility of the subsequent measurements. Ask yourself: are there enough test measurements at hand to be sure that the protein is still happy and intact? In bad cases, proteins may not survive storage for one hour at room temperature...
The list of possible problems when handling proteins is long and well known to people in the field, but because we get used to ordering oligonucleotides on a large scale, it appears that some people think we can treat proteins the same. It is not sufficient to buy a lyophilized protein, dissolve it, and begin experiments. Even if you are lucky, only 10 percent of the protein might be in an active conformation.
I have the impression that lab throughput has become so important that checking protein loss, purity, activity, agglomeration by gels, circular dichroism and folding melting temperature (to assess the quality and buffer conditions for the protein) has become a luxury. And let’s not forget the need to address and evaluate protein losses from pipetting and adsorption.
In reality, taking proper care of your protein samples is fundamental to performing solid science. Despite all the progress, proteins remain quite tricky to handle. I dearly hope that basic quality control in protein handling will gain the attention it deserves and start to improve again. Otherwise, bionalysis will not become more complex or quantitative, it will simply become noisier.
Dieter’s PhD adviser told him to avoid interdisciplinary research. “You will be caught between two stools and have a hard time to get funding and citations,” were his warning words. But there was no way he could avoid it. “I’m enjoying being right between the disciplines; the work is much harder, but so much more fun,” says Dieter, now Biophysics Professor at the LMU Munich. He performs origins-of-life research from a non-equilibrium perspective, a topic his PhD adviser was very interested in, but never dared to do. While funding is indeed difficult, the approach has paid off for two of his PhD students: Philipp Baaske and Stefan Duhr who own the protein quantification startup, Nanotemper, which has more than 70 employees.
