Why protein structures wobble like a cat

Ever wonder why a protein structure is wobbled like a cat in the shape of a hunk of cheese? Well, let me tell you, it doesn’t always make sense.

A recent paper from McGill University — which received a lot of media attention recently, including a whole two whole pages in Nature — investigates this type of happenstance, described as “negativity scattering.” Negativity scattering is simply an evocation of a food state, the type of complex matter that leaves its fingerprints everywhere. By manipulating a single molecule in a solution with negative configuration, a researcher can create a distinct scattering characteristic.

Over 100 researchers contributed to the published research, from academia, industry and government. Some have used the technique of negative scattering to examine the effects of cold, neutral water. In this study, negative scattering was used to study splicing errors in protein structures. These splicing errors affect the structure’s physical strengths, the specificities that certain individuals dislike or need.

There’s a lot to learn about the protein structures at work in our bodies. This study is one part of that endeavor.

The study found significant potential for negative scattering to provide insights into why certain splicing errors, such as those seen in maternal splicing errors, can go undetected. However, the authors caution that “In analyzing miscoding mistakes, we do not expect to discover the precise causes of their cellular specific presence.”

The paper posits that this has to do with splicing errors making splice regions either too small or too big for conventional measurements. In other words, there is some uncertainty with the hunk of cheese we call protein.

Now, most people are familiar with splicing errors in protein assembles, or assembly line proteins such as DNA, mRNA and proteins. Occasionally, the defective splicing will become explicit, which brings on “false positives.” In that case, the error has no effect but the “true” genes are turned off or down. Geneticists call this “false positive” splicing.

Research done a little earlier on a splicing error at the same protein’s ability to make a nucleus may help scientists clarify the strength of the negative scattering signature in its structure.

The authors also suggest that negative scattering shows up more in other areas of protein structure as well. For example, negative scattering might be associated with folds in dendrites and tentacles — places on complex protein structures that do not serve as actual structures. While those parts of the protein don’t seem to have much in common with the protein splicing region, negative scattering could become a useful marker. The authors, however, hope this could become a true clue for the field.

All of this may not sound very exciting, but the scientists involved are hoping that by digging deeper into some of these headier problems, they may soon find solutions.

This research builds on previous efforts to look at negative scattering in how protein splicing has occurred in the early stages of the protein assembly process. This is known as “functional atrophy.” In effect, the study’s authors are using positive scattering to look more deeply into the early stages of splicing.

This study used a high-speed confocal microscope system developed at McGill University to analyze the negative scattering marks on proteins. A negative scattering signature looks nothing like the signature you’d see if the protein were spliced but not divided.

The study, recently published in PNAS, brings to the fore more questions, but also more basic research. If this does help us understand what things could do in the future, it’s an eye-opening piece of the puzzle. While it may be not the golden solution, this study is providing some good hints for the future.

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