I went to the annual Protein Society symposium a few weeks ago and have finally had some time to organize my thoughts about it, so I figured I'd put some of them up here. Expect a couple of these to show up.
One of the most interesting presentations at the Protein Society (besides my own scintillating poster on field-cycling, haha) was Brian Volkman's poster on lymphotactin. This is a really interesting story that somehow seems to keep flying beneath the radar of most people, but intellectually it represents a giant challenge.
In a nutshell, the story is this: lymphotactin is a small signaling protein of the chemokine family, a group of proteins that are important for various kinds of regulation, including in inflammation and disease. Under fairly standard experimental conditions (200 mM NaCl, 10 °C) the protein adopts a normal chemokine fold, but at 45 °C (for reference, body temperature is 37 °C) and low salt, it takes on a totally different fold. You can read the original paper on this here. Of course, when you see something like this it's natural to ask what the physiological relevance of the finding is. Brian's poster at Protein Society basically answered this question by illustrating different biological roles for the two forms. The short version is that the conformational change appears to be some sort of regulatory switch. I'll have more on that in the next episode.
What I want to talk about here was what wasn't said about this at the meeting. After all, we were forced to witness the usual ninny-argument over whether folding was a linear pathway or a funnel of some kind. While it was refreshing to hear a lot more people pointing out that this distinction is more or less meaningless, it's odd that nobody is tackling the question through a protein like lymphotactin. Consider the following experiment: perform phi-value analysis or GdHCl-dependent HX experiments on lymphotactin to find what portions of the protein are structured in the folding transition state. We can imagine two outcomes.
In the first, the transition state is found to be completely different; that is, residues with high phi-values or the last residues to lose protection in the HX experiment are completely different for the two conformations. This would suggest that the latest common intermediate is the random coil (RC), and that the very first move towards a folded state dictates the state one finally arrives at (N1 or N2). Any intermediates (I1 and I2) along the pathway are unique to the end state, rather than shared between the two conformations (see right). This would fit most closely with the pathway view promulgated by Englander. Given that the hydrogen-bonding patterns are totally different for the two conformations, this might be expected.
On the other hand, it's possible that a residue or cluster of residues have similar phi-values, or lose their protection at a similar GdHCl concentration, between the two conformations. This would not be completely probative, as the similarities could quite easily be restricted to the observables and represent two different underlying structures. However, if veridical this might suggest that the latest common intermediate lies somewhere other than in the random coil. This would be more similar to the funnel view, in which a conformational search over the outcomes available to an intermediate gives rise to the ultimate choice of native structures. I've cartooned the idea over to the left. In this case I* represents a partially-folded intermediate that selects an end state based on the conditions.
After all, lymphotactin in both its native forms exists in physiological extracellular conditions. Knowing whether the protein must pay the full energetic cost of completely unfolding, or if it can switch conformations by taking a less-costly move to a common intermediate may be of significance to understanding the biology. And while these two alternatives (like the underlying models) are not as different as they may seem of first blush, the answer may do much to distinguish whether the conformational search of the funnel model or the deterministic folding of the pathway model is the best representation of the folding process.
Another major implication here is for the protein structure prediction crew. After all, the CASP-type experiments are all geared to the idea that a given sequence should give rise to a single folded structure. Lymphotactin is a clear counterexample to this idea, and while it may be unique, we certainly don't know nearly enough about proteins to let the dogma go unquestioned at this point. This makes for a much larger computational problem. I'm not a huge expert on these experiments, but my impression is that the programmers don't concern themselves too much about the characteristics of the solution the proteins are in. The assumption that co-solutes don't much matter is vastly simplifying, but as Brian's work shows, may ultimately limit the predictive power of these algorithms in significant ways.
One of the most interesting presentations at the Protein Society (besides my own scintillating poster on field-cycling, haha) was Brian Volkman's poster on lymphotactin. This is a really interesting story that somehow seems to keep flying beneath the radar of most people, but intellectually it represents a giant challenge.
In a nutshell, the story is this: lymphotactin is a small signaling protein of the chemokine family, a group of proteins that are important for various kinds of regulation, including in inflammation and disease. Under fairly standard experimental conditions (200 mM NaCl, 10 °C) the protein adopts a normal chemokine fold, but at 45 °C (for reference, body temperature is 37 °C) and low salt, it takes on a totally different fold. You can read the original paper on this here. Of course, when you see something like this it's natural to ask what the physiological relevance of the finding is. Brian's poster at Protein Society basically answered this question by illustrating different biological roles for the two forms. The short version is that the conformational change appears to be some sort of regulatory switch. I'll have more on that in the next episode.
What I want to talk about here was what wasn't said about this at the meeting. After all, we were forced to witness the usual ninny-argument over whether folding was a linear pathway or a funnel of some kind. While it was refreshing to hear a lot more people pointing out that this distinction is more or less meaningless, it's odd that nobody is tackling the question through a protein like lymphotactin. Consider the following experiment: perform phi-value analysis or GdHCl-dependent HX experiments on lymphotactin to find what portions of the protein are structured in the folding transition state. We can imagine two outcomes.
In the first, the transition state is found to be completely different; that is, residues with high phi-values or the last residues to lose protection in the HX experiment are completely different for the two conformations. This would suggest that the latest common intermediate is the random coil (RC), and that the very first move towards a folded state dictates the state one finally arrives at (N1 or N2). Any intermediates (I1 and I2) along the pathway are unique to the end state, rather than shared between the two conformations (see right). This would fit most closely with the pathway view promulgated by Englander. Given that the hydrogen-bonding patterns are totally different for the two conformations, this might be expected.
On the other hand, it's possible that a residue or cluster of residues have similar phi-values, or lose their protection at a similar GdHCl concentration, between the two conformations. This would not be completely probative, as the similarities could quite easily be restricted to the observables and represent two different underlying structures. However, if veridical this might suggest that the latest common intermediate lies somewhere other than in the random coil. This would be more similar to the funnel view, in which a conformational search over the outcomes available to an intermediate gives rise to the ultimate choice of native structures. I've cartooned the idea over to the left. In this case I* represents a partially-folded intermediate that selects an end state based on the conditions.After all, lymphotactin in both its native forms exists in physiological extracellular conditions. Knowing whether the protein must pay the full energetic cost of completely unfolding, or if it can switch conformations by taking a less-costly move to a common intermediate may be of significance to understanding the biology. And while these two alternatives (like the underlying models) are not as different as they may seem of first blush, the answer may do much to distinguish whether the conformational search of the funnel model or the deterministic folding of the pathway model is the best representation of the folding process.
Another major implication here is for the protein structure prediction crew. After all, the CASP-type experiments are all geared to the idea that a given sequence should give rise to a single folded structure. Lymphotactin is a clear counterexample to this idea, and while it may be unique, we certainly don't know nearly enough about proteins to let the dogma go unquestioned at this point. This makes for a much larger computational problem. I'm not a huge expert on these experiments, but my impression is that the programmers don't concern themselves too much about the characteristics of the solution the proteins are in. The assumption that co-solutes don't much matter is vastly simplifying, but as Brian's work shows, may ultimately limit the predictive power of these algorithms in significant ways.
1 comment:
I don't understand any of these, but it amuses me that you have a society for your proteins.
Post a Comment