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How do Regulatory Sites Communicate with Active Sites in Regulatory Enzymes?

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How do Regulatory Sites Communicate with Active Sites in Regulatory Enzymes?
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Without disrespect or exaggeration, we may characterize William Lipscomb as the member of a relay team that created knowledge on the nature of chemical bonds and the course of chemical reactions and carried it forward through time. He received the baton from his teacher Linus Pauling, recipient of the Nobel Prize in Chemistry 1954 "for his research into the nature of the chemical bond and its application to the elucidation of the structure of complex substances", and passed it on to his student Roald Hoffmann who shared the Nobel Prize in Chemistry 1981 with Kenichi Fukui for his theories „concerning the course of chemical reactions“. His own studies on the structure of boron hydrides (boranes), which did not only determine the structure of those compounds but also illuminated general problems of chemical bonding, began in the early 1950s and earned him the Nobel Prize in Chemistry 1976. Pauling’s mentorship meant much to him, as he humorously remembers in this Lindau lecture: „He told me on boronhydrates and I knew everything he told me was wrong, and I learned from him that it’s not so bad to be wrong. It’s bad to be uninteresting! Because his ideas have been stimulating!“ Combining quantum mechanical calculations and means of X-ray diffraction was one of the hallmarks of Lipscomb’s borane research project. Therefore it was only natural that in the decades after the reception of his Nobel Prize he began to focus on X-ray crystallography. He elucidated the structures of large and complex enzymes and analyzed their mode of action. In this lecture, he talks about the function and regulation of two enzymes he had recently studied in his laboratory: Fructose-1,6-biphosphatase and aspartate carbamoyltransferase. The latter catalyzes the first step in the biosynthesis of pyrimidines. „About six steps down the metabolic pathway there is generated cytidine triphopshate, which is a precursor of DNA and RNA - one of four - and it inhibits the enzyme at a site which is 60 angstrom away from the active site.“ Lipscomb describes in detail the interplay between these two and other binding sites of this 300 kiloDalton enzyme with its twelve subunits, which is today regarded as „an archetypal example of allosteric modulation of fine control of metabolic enzyme reactions“.[1] Fructose-1,6-bisphospatase is a key enzyme in gluconeogenesis and helps to fill our glycogen reservoir. „You need it to come through the night“, says Lipscomb. Its opponent is phosphofructokinase, which catalyses the reverse reaction (i.e. phosphorylation) in glycolysis. To avoid simultaneous anabolic and catabolic activity at the same pace in the same place, both enzymes therefore need tight control. Fructose-1,6-biphospatase is controlled at its active and at an allosteric regulatory site. Lipscomb illustrates in atomic resolution how these control mechanisms work. Inhibition of fructose-1,6-bisphospatase at its allosteric regulatory site by compounds that mimic AMP but bear little structural resemblance may prove to be an effective treatment for type 2 diabetes, he explains, and mentions that he is collaborating with a pharmaceutical company to develop such an inhibitor. Lipscomb’s latest paper on this subject stems from the year 2005 (when he was 85 years old)[2], and while fructose bisphospate inhibitors have not been approved yet, they are still regarded as a potentially important class of novel antidiabetic agents. Joachim Pietzsch [1] Aspartate carbamoyltransferase. (2014, January 14). In Wikipedia, The Free Encyclopedia. Retrieved 19:14, June 15, 2014, [2] Erion MD, van Poelje PD, Dang Q et al. MB06322 (CS-917): A potent and selective inhibitor of fructose 1,6-bisphosphatase for controlling gluconeogenesis in type 2 diabetes. Proc Natl Acad Sci U S A. 2005 May 31;102(22):7970-5.
Hope, ArkansasChemistrySet (abstract data type)Golgi apparatusGrading (tumors)Chemical experimentMeeting/Interview
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BoronPauling, LinusHydrideMeeting/Interview
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Transcript: English(auto-generated)
Thank you very much for the kind introduction. It's my fifth visit to Linda Ahn. I'm so pleased to be here to talk to you.
I don't know that I should give you any advice. My mother gave me a chemistry set when I was 12 years old. I hope that the legal profession still allows people to do that without lawsuits. It's a little difficult in our country because, but I hope you can still get chemistry sets. I accumulated a lot of apparatus,
and when I went to my high school, the 11th grade, my teacher said, oh, don't bother to come to class. Just take the final examination, and I sat in the back of the room doing a little research project that I invented.
I learned from that that you should never let schools interfere with your education. And I also did a research project when I was an undergraduate, and I found that I was doing not very interesting research projects.
So I went to graduate school at Caltech, and I learned from Linus Pauling what were really interesting problems to work on. And I think it's a good idea to work with someone who knows things and is really doing forefront of research. And of course, that's one of the reasons you're here to learn about that.
He told me about boron hydrides, and I knew everything that he said was wrong. And I learned from him that it's not so bad to be wrong. It's bad to be uninteresting because his ideas have always
been very, very stimulating and nearly always right. It also helps to have very good students, and I point out that my best, most well-known student is Roald Hoffman. So this brings me to the talk, which
is in an area that I've been working in with my students for almost 30 years. When we look at the 300 enzymes that are known, very few of these are enzyme complexes.
Many enzymes, there was a reference in Johan Deisenhofer's talk to complexes of P450, but many of the biological systems require complexes of proteins with other proteins.
And Sir John Eccles referred to this in his talk, where many of the complexes are of unknown structure. We have so far to go. The particular area where complexes are important that I'm talking about is enzymes that change structure in order to modify the function.
Now, there's an illustration. I'll talk about two enzymes from my laboratory. The first is fructose 1,6-bisphosphatase, and that enzyme is in the gluconeogenic pathway.
It takes three carbon systems and makes glucose, and you need it to get through the night because your blood cells and brain need glucose, and you run out of it. So that's opposite to the glycolysis pathway. Now, you realize that in this, here's this enzyme, and what it does is remove the 1-phosphate
from fructose 1,6-diphosphate to make fructose 6-phosphate and phosphate inorganic. And there is an opposing enzyme in the glycolysis pathway that makes eventually carbon dioxide and water
and ATP along the way. And here, if you imagine that these two enzymes are allowed to proceed, that you use up ATP for no purpose whatsoever, and this requires very precise control. So this enzyme has an active site inhibitor,
which is fructose 2,6-diphosphate, and it also has an inhibitor at a different site, which is completely different structure from the substrate, which is 1,6-diphosphate, not 2,6. This is a different structure and therefore called
allosteric by Monod and his coworkers. Now, the enzyme has a metal, two metals at the active site in the active form magnesium, manganese, or zinc, mostly manganese and zinc in physiological systems.
And what the AMP does is to change the conformation of the enzyme completely so that it reduces the binding of the catalytic metal, but it does not affect the binding of the substrate, and that's the bottom line here. So this is what the enzyme does.
Now, we've worked on the pig kidney enzyme, which is a tetramer of 335 amino acids times 4 for the tetramer. It is active in the tetrameric form, about half as active in the dimeric form,
and not regulated by AMP. So the regulation requires a tetrameric form. Here is the tetramer, and the active site is in blue. The regulatory sites are in yellow, 30 angstroms between the nearest ones, and beside the active site is at least one metal site
shown by a star here. Now, in this region, a large conformational change takes place, as I shall describe, but I'm first going to examine the reactivity, but while this is here, I point out all this pleated sheet.
And right there is the pleated sheet, and here it is again right along here, and three helices in each monomer, three here, three here, and three here, and those shift a little bit during the transformation, and that's where the regulation is.
The monomer is shown here with the active site, and here is the regulatory site adenosine monophosphate. There are helices and beta structure, pleated sheet structures of the form that Pauling originally proposed, and he was absolutely right about that,
and made a big advance in proposing the helical structures and pleated sheet structures, which are shown schematically here. The substrate is the alpha anomer of fructose 1,6-diphosphate. The beta anomer here, which in solution is 80%,
in an equilibrium, is not the substrate, and that was shown by Benkovic, who did some very nice kinetic work, that the enzyme chews up this molecule rapidly, and then it settles down after 20% of the substrate is gone, and slows down to a rate
which is exactly the rate of interconversion in solution, uncatalyzed. Next. Now, this is the alpha anomer again, and of course, at least at present in X-ray diffraction, you cannot work with real substrates,
you have to work with an inhibitor which resembles the substrates, and it turns out that the two prime hydroxyl group is critical for activity of the enzyme, and if you remove it and make this analog, then you have a nice inhibitor, and this is the way it's bound in the active site,
and it takes on two zinc atoms, about four angstroms apart, three and a half angstroms apart here. So here is the 6-phosphate, and here's the ribose ring, and here is the 1-phosphate of this inhibitor in this region.
If you take the beta anomer, then again, you remove the hydroxyl group, which is now in this position in the beta anomer, then here it is, the two prime hydroxyl group, then you have only one metal bound,
and this is inactive. So presumably the activity, at least for manganese or zinc, is associated with the second metal. This is a little more extended, and the structure in this region is slightly different,
but the structure up here, the 6-phosphate and the ribose ring, is the same in product in many other inhibitors that we've studied. Next slide. And here is then the first part of the talk on activity alone, and this is a picture of the 6-phosphate,
how it's bound, the ribose, and here is the critical hydroxyl group, which is near aspartic 121, and which is near this oxygen, where cleavage will take place to make a phosphate,
and presumably the proton is transferred here. There seems to be no other way for this oxygen to accumulate a proton, and for this group to leave. Now in this position, where there is a question mark, we do not see a water molecule, but if a water molecule came in here,
we would have an in-line attack with an inversion of configuration at the phosphate, when the phosphate is formed, you get inversion, and that is exactly what is observed in Benkovich's experiments, that you get inversion of the phosphate, so I think this is probably a good model for the active activity of the enzyme.
Such acid groups, there's aspartic 121, glutamic 97, aspartic 118,
and are involved in the activity here, and they are the residues which undergo conformational change in the T to R transformation. So the active site binds both anomers, the substrate is the alpha anomer,
two metal sites are at the active site, and the manganese and zinc complexes, but only one is in the magnesium complex, the binding, there's a binding sequence, and substrate hydrolysis occurs by direct nucleophilic attack by a metal coordinated water at the phosphate center.
Aspartic acid 121 probably acts as a general acid, and the two prime hydroxyl group serves as a proton donor. That's our present hypothesis. There are few places in chemistry where you almost see your reaction in three dimensions, and what we supply then is a picture which can be tested with tracer work
and mutagenic work and so on, so it's only the beginning. Now on the next, I show the conformational change, and it's a large one. There's a 17 degree rotation of one dimer with respect to the other dimer,
and the monomer which is shown here, the less active form in yellow, the more active form in blue under has some conformational changes, and they are mostly confined to this area where the pleated sheet exists, and the three helices exist.
The AMP site is here. This is the allosteric regulator, and the active site is here 30 angstroms away. The big change that takes place is induced by adenosine monophosphate, which is shown here in one monomer,
and here in the other monomer, and this is the less active form on the left and the more active form on the right. Again, adenosine monophosphate here and in the other monomer here on the interface where the three helices are here in this monomer, here in this one,
and the pleated sheet is not shown. It's just a little behind here. So it's the binding of AMP that makes this shift, and the communication occurs through the helices and the pleated sheet, which extend from the regulatory site to the active site,
and they're affected differentially. The movement is not a complete unit. The different groups rotate slightly differently as the 17-degree rotation takes place of one dimer with respect to the other.
Here are the three helices, one, two, three here, and then the pleated sheet, you can see the strands of pleated sheet, and this is the active site, aspartic 121 I pointed out, and then this is with product,
fructose-6-phosphate in here, that's the phosphate and the fructose, and here is the regulatory site over here. And shifts take place in the binding of these residues, threonine-27, lysine-112,
and here's the AMP and tyrosine-113, and they connect to one of the strands of pleated sheet. And while the dimer rotates 17 degrees, the helices rotate 14, 12, 16. They rotate different amounts. On the average, 14 degrees, as compared with 17 degrees, and over 30 angstroms,
that makes some distance change. Here's their degrees of rotation. Next, next to Bill. And this 17-degree rotation results in a shift of about one angstrom in the adenosine monophosphate domain,
relative to the fructose, the active site, the fructose bisphosphate domain, which is here. There are other interactions that occur if you cleave this loop 55 to 60, which was the one which made the big conformational change.
The AMP is no longer effective. Now, the movement of the metal is not very great. The movement of metal and active site residues, the movement of the C office of these residues, here's aspartic-121 again,
and that one, the side chain, however, moves four angstroms when you go through the conformational change. That then makes it impossible for the metal to bind in the AMP form, the less active form. Next slide.
That completes this story, except for this rather interesting molecule here, which is a histidine with an amide and an amino group on resembling AMP. These people have published a paper
in which this molecule is shown to inhibit the synthesis of glucose in rats. And I'm working with a company now who is trying to make a good many analogs of this is the lead compound. It needs a higher concentration.
It's not toxic. It needs an improvement in the binding in various directions that we can see on the enzyme surface, and we hope will be useful in treating type 2 diabetes. I think this is one of the possible practical aspects of this structure determination.
This is a new method of designing drugs, which was inaugurated by the use of carboxypeptidase, one of our other enzymes, to design captopril, which inhibits angiotensin-converting enzyme, to control high blood pressure. So that the use of these three-dimensional structures
to design inhibitors that block pathways, or at least reduce the activity in pathways, is a new method of drug design, which was unavailable before the protein structures were obtained. And I want to acknowledge at this point my coworkers in this field.
Next slide. Now, I come to the second enzyme that I want to talk about today, which is aspartate trans-cobamylase, which we've been working on a long time. And what it does is to start the pyrimidine pathway, and this is the E. coli enzyme.
Carbamyl phosphate reacts with aspartate. You lose a proton, and the pair of electrons then attacks the carbon, and phosphate leaves. And the first part I'll talk again about the activity,
and then later I will talk about the regulation. Now, I'll abbreviate carbamyl phosphate as CP. Here's aspartate, carbamyl phosphate. This is the catalytic mechanism. About six steps down the metabolic pathway, there is generated cytidine triphosphate,
which is a precursor of DNA and RNA, one of the four, and it inhibits the enzyme at a site which is 60 angstroms away from the active site. Now, in the language of Manot, Chenzhou, and Weiman,
the homotropic effects means that there is a less active T form of the enzyme. T means tense, but it's not quite a good nomenclature. The T form of the enzyme has already carbamyl phosphate on it because in the physiological medium, carbamyl phosphate is at such a concentration
that it's saturated, and aspartate then makes the big confirmation to the more active R form. This is a conformational change in the absence of the regulators, cytidine triphosphate, and which inhibits the enzyme, and adenosine triphosphate,
which activates the enzyme, and these are called heterotropic effects because these do not look like a substrate. Now, there has been a discussion in the literature for 25 years and more about whether changes in the enzyme are concerted or whether they're sequential,
and I think in the structure field we'll probably end up saying that they're mostly one way or partly one way, but not completely. And in this case, it is most likely that the homotropic effects are mostly concerted,
and the heterotropic effects are mostly sequential, but the story is almost certainly in between. In the original Mano-Chaunge-Wiman paper, there was no provision for negative cooperativity, and that is not in agreement with the theory. This enzyme shows negative cooperativity.
Now, positive cooperativity means if you bind the first molecule, then it has difficulty binding to the less active form to make the conformational change that activates the other active sites. That's positive cooperativity. So, the first molecule goes on with difficulty,
the second molecule goes on much easier. Hemoglobin is a perfect example, the original example, in which the first oxygen goes on with difficulty, the other three then go on much more easily. In negative cooperativity, it's just the opposite. The first molecule goes on more easily, and the rest go on with much more difficulty.
And that can be because either the enzyme is intrinsically asymmetric with respect to the binding sites for, in this case, cytidine triphosphate, or that the first molecule induces a conformational change, which makes the second one more difficult to bind.
In the case of this enzyme, the molecule is intrinsically unsymmetrical. In the next slides, I show you the picture of the enzyme. It has a trimer up here. The molecular weight's 310,000. The trimer is about,
here's the trimer up here, and another trimer down here. This is the less, actually, that's the less active form of the enzyme, and this is the more active form, which is more open. This trimer moves with respect to this trimer,
11 angstroms, which is a very large conformational change, and the dimers here are shown in yellow. They are the regulatory sites here and here on the outside of the trimers, and there's the third trimer behind there. Now, there's a loop, which I'm going to refer to frequently,
the 240s loop, 235 to 245, and that has a tyrosine, a particular tyrosine that I'll talk about. That loop undergoes a very large conformational change, and it turns out the tyrosine 240 is attached directly to
one of the residues that binds the substrate. This enzyme regulates, not by modifying the catalytic rate, but by modifying the binding of substrate, and the arginine that is affected by this undergoes a very large conformational change,
a change in the side chain conformation when the effectors bind, when cytidine triphosphate pulls it away, and adenosine triphosphate pulls it into the active site, and this is the way the regulation takes place, and it is the binding step that is affected. That loop is now in a different position,
so anything that induces a conformational change will force this loop to make a conformational change that is large. Here is another look. The catalytic trimer is here, and here is, this is the less active form. Tyrosine 240 is marked with an asterisk here,
a little star, and here is the other catalytic trimer. The regulatory dimers are here and here. One interface, the C1R4 interface, or the C4R1 interface, disappears completely in the more active form. The other interfaces do not change very much,
but there are some changes. And here is a monomer, the catalytic monomer. There's catalytic protein and a regulatory protein, and each catalytic protein has two domains which close when the substrate binds,
and the closure makes a big change in the 240's loop, which is here in the blue in the more active form and in the red in the less active form. This is about eight angstroms motion of this side chain. There's a conformational change over here,
but this is because the active sites are shared between the units of the catalytic trimer. This points to the active site of another one of the trimer, another active site in the trimer. So there is, in this active site,
there's another one of these coming from a different catalytic chain of the trimer. So we have conformational changes here and here. Next, next to Bill. In the active site then, we bound phosphone, this phosphone acetyl group. This is aspartate. This looks like aspartate with an alpha and beta carboxylate group,
and then you go along. This almost resembles carbonyl phosphate, except that the phosphate is now bound through a CH2. So this is a phosphonate, and the enzyme cannot cleave this bond. It cleaves PO bonds, but it doesn't cleave PC bonds,
and so this is a very strongly bound inhibitor, which is sometimes, which is on the market for cancer chemotherapy, and here are the binding groups, and here's the serine and lysine that come from an adjacent catalytic chain over here.
The enzyme is very specific for aspartate as the amino acid to be carbamylated, and it is this arginine 229, which undergoes the largest conformational change in the active site.
All of these groups have been mutated, and the indication from that is that we really are at the active site, and this very strongly bound 10 to the minus 8th dissociation constant, 10 to the minus 8th molar, this is surely in the active site. In fact, we've actually bound carbamyl phosphate,
which binds as shown over here, very much like this, and instead of aspartate, we've used succinate, which doesn't have the NH2 group, but if you put the NH2 group on here, it's in a perfect position to attack the carbamyl carbon, so this is a good model for the reaction.
Next slide. And when you look at the enzyme, there is no group which carries out the critical step in the reaction, no group on the protein, that is the removal of this proton from the NH2 group,
that's the most difficult step, and the only group that, sorry, this one, the removal of the proton from the amino group is the critical step in the formation of this bond between the nitrogen and the carbon here.
So what we've done then is to notice that the group which is nearest, three angstroms away, is an oxygen of the phosphate, and so we have proposed this mechanism in which the lone pair attacks, and a proton is transferred to here, and again this bond is cleaved, so it's just a little cyclic step,
and this is open to test, but it shows that when you look at an enzyme structure and imagine the reaction, you sometimes can guess and sometimes not. So we present this to the biochemical community for their isotope tracer work
and other mutagenic studies to see if this is a correct mechanism. I think it's probably right. The activity, again, this is a curve which shows positive cooperativity. The first substrate, the velocity of the reaction in this way, the molarity of aspartate is out this way.
The other substrate, carbonyl phosphate, is saturating the enzyme, so we vary only one. The first, the reaction does not speed up very much when the first substrate is bound, but after the next ones bind much more easily,
and cytidine triphosphate inhibits the enzyme, adenosine triphosphate stimulates the enzyme. Now this is a regulatory monomer showing the regulatory site with cytidine triphosphate,
and there are several contacts between this regulatory chain, two domains, an allosteric effector domain, a zinc domain, and a place in between, which is shown here, in which some hinge motion takes place.
It bends a little bit when the CTP and ATP modify the activity. Another communication between C1 and R1 is this, this area here, which is arginine-130 and glutamic-204
from the catalytic chain, and the active site is over here. There's a zinc site, but zinc is structural. It is not involved in the catalytic steps. Hervé in Jiffes-sur-Yvette in near Paris, and Qunin,
Raymond Qunin from Brussels, have modified one other tyrosine residue, tyrosine-77 in the regulatory chain, just the removal of the hydroxyl group. They made it phenylalanine in the mutation, and it changes adenosine triphosphate completely from an activator to an inhibitor.
It's a very striking result. It's the most striking mutation that has been made. So this interface, which is right here between the two domains, the zinc domain and the allosteric effector domain, is important in the regulation of the enzyme. Now in the T to R transition,
let me summarize. The catalytic trimers rotate with respect to each other 12 degrees. That is, if you hold one fixed, the other one rotates 12 degrees. They separate by 11 angstroms, and the regulatory dimers rotate 15 degrees
about the almost two-fold axes of the molecules. The two-fold axes are not perfect. There's a problem? Oh, time. I see. Yes. So what we have then is that the cytidine triphosphate
we find contracts the R structure by half an angstrom, and ATP expands the structure by half an angstrom. And it is this action on the R1-R2 interface, which when you close it, it makes the enzyme close. When you close the regulatory dimer,
the enzyme comes together and makes the T form. When you open it, it causes the enzyme to go to the R form. And that's the essence of the conformational change. Now I have some more slides, but what I'd like to do is proceed to the last slide. Just keep going.
Okay, this is, well, let me just stop here because it's my acknowledgement. And to tell you that we are now doing pH studies with the synchrotron so you can pulse the protons, and you can take complete three-dimensional data in 300 milliseconds. That's really a very striking advance.
And finally, I really don't hesitate to show the last slide, but I think at every talk in Germany should have a quotation from Goethe. So I show you the following quotation. Next. Next inbuilt.
What happened to my quotation from Goethe? It's in there somewhere. There it is. I see you.
Thank you, Professor Lichten, for this very nice talk. And I'm sorry that a problem which is not a problem which is not a problem which is not a problem which is not