Monday's Molecule #67

 
This is a very important protein. Most living organisms on this planet could not survive if this protein didn't do its job.

Your task for today is to identify the protein (1) and the species from which this particular protein was isolated (2). You also have to describe the function of this protein (3).

In addition you have to identify the Nobel Laureate who was awarded a Nobel Prize for—among other things—working out the structure of this protein. Note that the protein is a tetramer (quaternary structure) showing a nice example of a helix bundle.

The first person to correctly identify the protein, species, and function, and name the Nobel Laureate. wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first collected the prize. There are two ineligible candidates for this week's reward.

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly answers the questions and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Laureates so you might want to check the list of previous Sandwalk postings.

Correct responses will be posted tomorrow along with the time that the message was received on my server. I may select multiple winners if several people get it right.

Comments will be blocked for 24 hours. Comments are now open.

UPDATE: We have a winner! Matthew Sekedat of Rockefeller University knew that this molecule was the potassium pump from the bacterium Streptomyces lividans. The protein is responsible for pumping potassium ions across the cell membrane. The Nobel Laureate is Roderick whose lab solved the structure of the protein.

---

TV Ontario's Best Lecturer

 
I've been critical of the contest for best lecturer because it focuses on style and not on substance [TV Ontario's Best Lecturers]. A few months ago I posted the names and areas of expertise of the three judges. Here's who they picked.


You can see the winning lecture at Ontario's Best Lecturer 2008!. A lot of it discusses naturalism and supernaturalism. Listen for yourself and see if you agree with the judges selection.

---

Framing Atheism

 
Here's a video that presents statistics about atheism. Some of it makes me uncomfortable because the numbers can be very misleading. Is this an example of framing according to the ideas of Nisbet and Mooney? If so, to my mind it illustrates all of the bad things about framing that turn scientist off.

---

[Hat Tip: Friendly Atheist]

Free Cheesecake!

 
Canadian Cynic just recorded one million page views! Congratulations to whoever you are and to your equally mysterious co-bloggers. The blog is promising free cheesecake for everyone [ Cheesecake for everyone] but the catch is you have to find them first.

BTW, take a look at the statistics posted on the Canadian Cynic website. The average length of each visit is almost 6 minutes!!! This is a long time for most blogs. (It's about 1.5 minutes on Sandwalk and 26 seconds on Pharyngula.)

I wonder if the average visitor to Canadian Cynic is temporarily stunned by the language? Or perhaps by the stupidity of the blogging Tories?

---

One Protein - Two Folds

Michael Clarkson at Discount Thoughts posted a discussion of a paper published by Tuinistra et al. (2008) [Two folds for lymphotactin]. The interesting thing about this paper is that it describes a protein (the chemokine lymphotactin) that can adopt two very different folds under physiological conditions.

This is an exception to the general principle that a protein will adopt a single thermodynamically stable three-dimensional structure. Here's how Micheal Clarkson describes it ... (Please read his article.)
THEME:

More posts on
Protein Structure

This is an interesting and important finding because it is (so far) the only example of a protein adopting two completely different stable folds with no hydrogen bonds in common at equilibrium. Trivially, natively disordered proteins adopt multiple conformations under physiological solution conditions, and many proteins alter their conformations in response to ligand binding while keeping most of their hydrogen bond network intact. In this case, however, an existing network of stabilizing bonds is completely disrupted in order to form a new fold with a totally different function. I've already discussed some of the implications of this with respect to protein folding, and in regards to the recent transitive homology studies out of the Cordes group. Lymphotactin offers lessons and ideas for protein folding and evolution that must be taken into account. In particular, the fact that point mutations can significantly stabilize one or the other of these structures implies that there may be previously unsuspected shortcuts through structural space between folded states that avoid unproductive or energetically unfavorable molten globules.

In addition, these results signify that the Anfinsen paradigm that dominates our understanding of protein structure ought not be taken for granted.¹ In many cases it is true that a peptide sequence uniquely determines a single structure under all physiological conditions. Of course we have known for some time that certain peptide sequences do not produce ordered structural ensembles at all. What the lymphotactin example makes crystal clear is that a given sequence can yield an ensemble with multiple energetic minima that reflect related but topologically distinct structures. Tuinstra et al. suspect that this phenomenon has not been noted previously because structures of this kind would not be amenable to crystallization, or would only crystallize in one (of many) structures. If this is so, then as more and more proteins are studied using solution techniques under physiological conditions we may find multiple structural minima in a variety of proteins. Such discoveries may significantly enhance our understanding of the protein regulation, function, and evolution.

Why is this important? Because this example demonstrates that getting from one type of fold to another type of fold isn't as big a problem as most people think.

The key phrase in Michael Clarkson's explanation is, "In particular, the fact that point mutations can significantly stabilize one or the other of these structures implies that there may be previously unsuspected shortcuts through structural space between folded states that avoid unproductive or energetically unfavorable molten globules." As we will see, the Intelligent Design Creationists argue that it is impossible to evolve from one type of protein to another, therefore God must have done it.

Incidentally, it's worth noting that some proteins adopt different conformations when they bind to other molecules (the target they bind to is called a "ligand" and it could be DNA, another protein, or a small molecule like ATP). Michael Clarkson mentions this—he appears to be a pretty knowledgeable guy—but I just want to repeat it so that everyone understands. The idea that parts of a protein (motifs, domain) can change folds under certain conditions isn't new.

---

1. I would prefer to say that, like all general concepts in biology, there are exception to the Anfinsen paradigm. I don't believe there are any fundamental concepts that don't have exceptions. That's the nature of biology, and evolution.

Tuinstra, R.L., Peterson, F.C., Kutlesa, S., Elgin, E.S., Kron, M.A., and Volkman, B.F. (2008) Interconversion between two unrelated protein folds in the lymphotactin native state. Proc. Nat. Acad. Sci. (USA) 105:5057-5062. [doi: 10.1073/pnas.0709518105]

Levinthal's Paradox

Back in 1969, Cyrus Levinthal was thinking about protein folding (Levinthal, 1969). He wondered how long it would take for a protein to fold correctly if it had to sample all possible conformations in three-dimensional space.

THEME:

More posts on
Protein Structure
Imagine that there was only a single bond between each amino acid in a protein of 101 amino acid residues. Imagine that there were only three possible configurations around each of those bonds. This means that the protein could adopt 3¹⁰⁰, or 5 × 10⁴⁷ different conformations.

If the protein is able to sample 10¹³ different bond configurations per second then it would take 10²⁷ years to sample all possible conformations of the protein (Zwanzig et al. 1992). This is quite a long time. Far longer, in fact, than the age of the universe.

Small proteins usually fold spontaneously within seconds and even the largest proteins fold within minutes. The difference between the theoretical calculation and the observed result is known as Levinthal's Paradox.

It isn't really a paradox. Levinthal knew full well that proteins did not fold by sampling all possible conformations. He knew that protein folding involved local cooperative interactions such as formation of α helices and that the formation of such secondary structure elements proceeded in parallel and not sequentially as his thought experiment proposed.

We now know that protein folding is largely driven by hydrophobic collapse as the regions of secondary structure come together to exclude water. This process is a global process involving simultaneous rearrangements of hundreds of bonds at the same time. That's why proteins fold so rapidly. Cyrus Levinthal knew this.

The point of Levinthal's paradox is to demonstrate that when a mathematical calculation shows that some routine process is impossible, then it's the calculation that's wrong, or the assumptions behind the calculation. This point is lost on most Intelligent Design Creationists. They are tremendously fond of complex calculations proving that some biological process is impossible. To them, this is not proof that their calculations are flawed—it's proof that a miracle occurred.

---

Levinthal, C. (1969) How to Fold Graciously. Mossbauer Spectroscopy in Biological Systems: Proceedings of a meeting held at Allerton House, Monticello, Illinois. J.T.P. DeBrunner and E. Munck eds., University of Illinois Press Pages 22-24 [complete text]

Zwanzig, R., Szabo, A. and Bagchi, B. (1992) Levinthal's paradox. PNAS 89:20-22. [PNAS]

Michael Egnor Gets It Right

 
Michael Egnor has posted a number of quotations from me about how I would deal with people who don't understand the basic principles of science [Dr. Larry Moran and Censorship of Intelligent Design].

He get it mostly right. If they are undergraduates who don't understand that evolution is a scientific fact, the Earth is 4.5 billion years old, and humans share a common ancestor with chimpanzees, then they flunk the course. If they are graduate students in a science department, then they don't get a Ph.D. If they are untenured faculty members in a science department, then they don't get tenure.

Readers might be amused at Michael Egnor's comments regarding Kirk Durston. It's further proof that IDiots are irony deficient. (Note that Kirk has not accepted my invitation to give a seminar here in the Biochemistry Department. I guess his "courage" has limits.)

Why should Mr. Durston’s willingness to present his scientific evidence for intelligent design to other scientists require courage? Isn't the presentation of evidence a routine part of science? Why should presenting evidence for intelligent design put Mr. Durston’s "scientific reputation on the line"?

Are you listening Kirk? Michael Egnor M.D. wonders why you don't come here and defend your evidence that protein folding demonstrates the existence of God.

I gave you two dates last November: you can give a seminar on Tuesday April 22nd or Tuesday April 29th.

---

Mike Huckabee Promotes "Expelled"

 
Were you wondering what Mike Huckabee was up to these days? No? Okay, then you probably won't be interested in this video ....


Why is there such a strong correlation between being stupid and believing in the Bible? How can a man like Mike Huckabee be seriously considered as a candidate for "leader of the free world?"

---

[Hat Tip: friend fruit]

Buy This Book!!!

 
Carl Zimmer is among the very best—possibly the best—of the modern science writers. His new book Microcosm: E. coli and the New Science of Life is going to be on sale May 6, 2008. Buy it, now. I just did.

Here's a synopsis from Publishers Weekly.

When most readers hear the words E. coli, they think tainted hamburger or toxic spinach. Noted science writer Zimmer says there are in fact many different strains of E. coli, some coexisting quite happily with us in our digestive tracts. These rod-shaped bacteria were among the first organisms to have their genome mapped, and today they are the toolbox of the genetic engineering industry and even of high school scientists. Zimmer (Evolution: The Triumph of an Idea) explains that by scrutinizing the bacteria's genome, scientists have discovered that genes can jump from one species to another and how virus DNA has become tightly intertwined with the genes of living creatures all the way up the tree of life to humans. Studying starving E. coli has taught us about how our own cells age. Advocates of intelligent design often produce the E. coli flagellum as Exhibit A, but the author shows how new research has shed light on the possible evolutionary arc of the flagellum. Zimmer devotes a chapter to the ethical debates surrounding genetic engineering. Written in elegant, even poetic prose, Zimmer's well-crafted exploration should be required reading for all well-educated readers. (May 6)

Copyright © Reed Business Information, a division of Reed Elsevier Inc. All rights reserved.

---

Having a Wife Creates More Housework for Men

 
A newly released study looks at the amount of house work done by men and women in different living situations. Like most of these surveys, the data is based on interviews and on diaries kept by men and women. The most remarkable results are reported in a press release from the University of Michigan [Exactly how much housework does a husband create?].

Here's how they describe the data collection process.

For the study, researchers analyzed data from time diaries, considered the most accurate way to assess how people spend their time. They supplemented the analysis with data from questionnaires asking both men and women to recall how much time they spent on basic housework in an average week, including time spent cooking, cleaning and doing other basic work around the house. Excluded from these "core" housework hours were tasks like gardening, home repairs, or washing the car.

Assuming that this is a reliable way of accessing workload, the study published a chart showing the amount of housework done by maried and single men and women.


The 2005 results show that when women get married they end up doing 7 hours more housework per week but when men get married they end up doing 8 hours more housework per week. The take-home message is clear. Women are a lot more costly than men. Women do more to mess up a house than men do.

Pay attention, men. It may not be worth the effort to get married.

The title of the press release is interesting: Exactly how much housework does a husband create?. Here are the opening paragraphs.

ANN ARBOR, Mich.---Having a husband creates an extra seven hours a week of housework for women, according to a University of Michigan study of a nationally representative sample of U.S. families.

For men, the picture is very different: A wife saves men from about an hour of housework a week.

The findings are part of a detailed study of housework trends, based on 2005 time-diary data from the federally-funded Panel Study of Income Dynamics, conducted since 1968 at the U-M Institute for Social Research (ISR).

Is it just me or does there seem to be a disconnect between the statements in the press release and the chart that's published on the same page?

---

Toronto Diversity

 
According to the latest census results, visible minorities make up 46.9% of the population of Toronto and 42.9% of the greater Toronto area. Check out the story in The Toronto Star and watch a video showing the change in precentage of visible minorities fro 1951 to 2006 [Visible minorities gaining].

How does this compare with other cities around the world? My impression is that Toronto is one of the more diverse cities in the world.

---

Ramachandran Plots

THEME:

More posts on
Protein Structure
The peptide bond has considerable double-bond character and this prevents rotation around that bond in the polypeptide chain. Adjacent amino acids can adopt different configurations by rotation around the two other bonds in the backbone. The angle of the bond between the nitrogen atom (blue) and the α-carbon atom (black) is &Phi (phi) and the angle of the bond between the α-carbon atom and the carbonyl carbon atom (grey) is Ψ (psi) [The Peptide Bond]. These angles are measured in degrees where 180° is the angle of the bonds when all of the atoms of both residues lie in the most extended conformation. Rotation in one direction is positive so the values go from 0° to 180° and in the other direction they go from 0° to -180°. (180° = -180° in this notation.)

Most of the amino acid residues in a given protein are found in some form of secondary structure such as α helix, β strands, or turns.

The Φ and Ψ bond angles for each residue in the α-helical structure are very similar as shown on the left. This is why the structure is so regular. Similarly, the Φ and Ψ bond angles for every residue in a β strand are similar. Since the residues in a β stand are in an extended form, the Φ and Ψ angles in this conformation are close to 180°.

For any given protein, you can plot all of the bond angles for every pair of residues. These can be plotted on a diagram called a Ramachandran plot, named after the biophysicist G.N. Ramachandran (1922 - 2001). Such a plot shows that most of the residues in β strands have similar bond angles that cluster in a region near the top left-hand corner of the diagram. Similarly, residues in a right-handed α helix have very similar bond angles around Ψ=-45°, Φ=+45°.

The residues in Type II turns also have very characteristic bond angles. Some regions of the Ramachandran plot will be empty because of steric clashes between the oxygen atoms [see The Peptide Bond]. These regions are mostly located in the lower right-hand corner of the plot.


Let's look at some specific examples. One of the proteins we saw in the slideshow was an all-α protein called human serum albumin [PDB 1BJ5]. Another was an all-β protein called Jack bean conconavalin A [PDB 1CON].


If you click on the PDB numbers of these proteins you will be directed to the Protein DataBase (PDB) entry for these proteins. Click on "Structural Analysis" then "Geometry" in the left-hand sidebar of these PDB entries to see the link to "Ramachandran plot." This will take you to the two diagrams shown below for Human serum albumin (left) and Jack bean conconavalin A (right).

The Ψ and Φ angles of every residue in the protein are plotted. Note that for the all-α protein (left) almost all the angles cluster around the region identified as α helix. Similarly, for the all-β proteins (right) the angles cluster in the upper left-hand corner of the plot where you expect to find residues in β strands.

Large regions of the plot are empty indicating that many conformations are disallowed for steric or thermodynamic reasons. The point is that the number of conformations of polypeptides in solution is not infinitely large. Most residues cluster in regions of secondary structure (α helix, β strands, turns). These are thermodynamically stable structures and polypeptides will spontaneously adopt these secondary structures very rapidly.

The overall conformation of a polypeptide then depends on the arrangement of secondary structure motifs relative to each other. Even at this level, there are preferred motifs such as β barrels and α helix bundles.

---

Come to Our Birthday Party!!

 
Click on Birthday Party for sharper images.

---

Get a Job!!

Position	Assistant Professor (2)
Location	Department of Biochemistry, University of Toronto
Position Description	The Department of Biochemistry, University of Toronto invites applications for two tenure-track positions at the rank of Assistant Professor commencing on July 1, 2008. The Department is interested in individuals who employ modern molecular approaches in studies of macromolecular complexes, membrane protein structure, lipid-protein interactions and dynamics, single molecule visualization and dynamics in living cells, non-coding RNA, or chromatin. Successful applicants will be expected to establish an independent research program, compete effectively for external funding, and contribute actively to the undergraduate and graduate teaching programs in the Department. Salary will be commensurate with qualifications and experience. Applicants should arrange to have three letters of reference sent directly to the mailing address below. In addition, applicants should send their curriculum vitae, copies of significant publications, and a 2-3 page description of their research plans either by e.mail to: chair.biochemistry@utoronto.ca or by mail to the address below. Closing date for applications is April 30, 2008, or until the positions are filled. The University of Toronto is strongly committed to diversity within its community and especially welcomes applications from visible minority group members, women, Aboriginal persons, persons with disabilities, members of sexual minority groups, and others who may contribute to the further diversification of ideas. All qualified candidates are encouraged to apply; however, Canadians and permanent residents will be given priority.
Eligibility	We seek candidates with a Ph.D. in biochemistry, biophysics, cell biology or a related discipline. Candidates must also have at least two years post-doctoral training and have an excellent publication record.
Contact	Interested candidates are encouraged to apply to: Chair, Department of Biochemistry Room 5205, Medical Sciences Building University of Toronto Toronto, Ontario, M5S 1A8, Canada.
Posted	March 13, 2008

---

The Peptide Bond

THEME:

More posts on
Protein Structure
Proteins consist of one or more strings of amino acids joined end-to-end to produce a polypeptide. The characteristics of each protein are due to the different amino acids that are combined to make the polpeptide(s). Each of the 20 or so common amino acids has a different side chain but the basic structure is common to all amino acids.

Amino acids have a central α-carbon atom, a carboxylate group (—COO^⊖), and an amino group (—NH₃^⊕). The fourth group attached to the α-carbon is the side chain (The third group is —H). Side chains can be as simple as —H (= glycine), or —CH3 (= alanine). In the example shown on the right, the side chain is —CH₂OH (= serine).

Proteins are synthesized by the translation machinery consisting of ribosomes , aminoacyl-tRNAs, and various translation factors. The template for synthesis is messenger RNA (mRNA) copied from the gene. Amino acids are strung together in a particular order specified by the mRNA codons.

The biosynthesis reaction is complex. It is coupled to hydrolysis of at least three ATP equivalents because the joining of two amino acids is thermodynamically unfavorable. The actual chain elongation reaction is catalyzed by the peptidyl transferase activity of the ribosome. The new bond that is created is called a peptide bond.


In the reaction shown above, the carboxylate group of the amino acid alanine is joined to the amino group of the amino acid serine to create a dipeptide with a peptide bond. Water is eliminated in this reaction. During protein synthesis the reaction continues as the mRNA is translated and long strings of several hundred amino acid residues are made.

The peptide bond has some interesting properties that play an important role in determining the three-dimensional structure of proteins. Look at the traditional depiction of the peptide bond in part (a) (top) of the figure on the left. It shows the actual peptide bond as a single bond and the bond between the carbon atom and the oxygen atom as a double bond. Note that the nitrogen atom has a pair of unshared electrons represented by the two red dots.

The middle structure shows that one electron from the nitrogen and carbon atoms can redistribute to form a double bond between C and N. This leaves an unshared pair of electrons on the oxygen atom. The actual bonding pattern is a mixture of these two resonance forms as shown in the bottom structure.

The partial double bond nature of the peptide bond has important consequences since it inhibits rotation around this bond. With a single bond there is free rotation so the groups on either side can adopt many different conformations. With a double bond there is very little rotation and the groups on either side are locked into the conformation that was formed when the bond is created.

The peptide bond has enough of a double bond characteristic to prevent rotation of the two newly joined amino acid residues. Thus, the O—C—N—H atoms around the peptide bond lie in a single plane shown in blue in the figure on the right.

What this means is the polypeptide chain is somewhat stiff and rigid. It can only adopt conformations that result from rotation around the other bonds in the chain. There are only two of these other bonds that can rotate. Looking at the central α₂ carbon atom above, you can see that there can be rotation around the N—C_α bond and around the C_α—C bond.

The angle of rotation around the N—C_α bond is called Φ (phi) and the angle around the C_α—C bond is called Ψ (psi). For each pair of amino acid residues, these two angles are all that's needed to specify the three-dimensional shape of the polypeptide backbone of the protein.

Not all angles are possible as shown on the left. If the two negatively charged oxygen atoms are too close together they will repel one another. This clash is called steric hindrance and it further limits the number of possible conformations of the polypeptide chain.

---