Chemistry posts

September 13, 2010
03:08 PM
699 views

Fishin' in the membrane

by The Curious Wavefunction in The Curious Wavefunction

Since we were talking about GPCRs the other day, here's a nice overview of some of the experimental challenges associated with membrane proteins and how researchers are trying to overcome them. These challenges are associated not just with the crystallization, but with the whole shebang. Although many clever tricks have emerged, we have a long way to go, and at least a few of the tricks sound like brute trial and error.To begin with, it's not that easy to get your expression system to produce ample amounts of protein. As indicated, you often need liters of cell culture to get a few milligrams of protein. The workhorse for production is still good old E. coli. E. coli does not always fold membrane proteins well, but it still beats other expression systems because of its cost and efficiency. Researchers have discovered several tricks to coax E. coli to make better protein. For instance it turns out that cold, nutrient poor conditions and slower-growing bacteria produce better folded and functional protein (although the exact reasons are probably not known, I suspect it has to do with thermodynamics and the binding of chaperones). Adding lipids from higher organisms to the medium also seems to sometimes help.What’s more interesting are efforts to do away with cellular production altogether and just add reagents to cell lysates to jiggle the protein-production machinery. For some reason, wheat-germ lysates seem to work particularly well. There are companies willing to use these lysates to produce hundreds of milligrams of protein. One of the advantages of such cell-free systems is that you can add solubilizing agents and detergents to stabilize the proteins. A striking fact emerging from the article is how many private companies are engaged in developing such technology for membrane proteins; the end "credits" list at least a dozen corporate entities. The list should be encouraging to visionaries who see more fruitful academic-industrial collaborations in the future.Then of course, there’s the all-important problem of crystallization. Of the 50,000 or so structures in the PDB, hardly a dozen are of membrane proteins. Membrane proteins present the classic paradox; keep them stable in the membrane and methods like crystallography and NMR cannot study them, but take them out of the membrane and, divorced from the protective effects of the lipid bilayer, they fall apart. Scientists have worked for years and come up with dozens of tricks to circumvent this catch-22. Adding the right kind of detergents can help. In the landmark structure of the beta-2 adrenergic receptor that was solved in 2007, the researchers used two tricks: attaching a stabilizing antibody to essentially clamp two transmembrane helices together, and replacing a disordered section of the protein with a T4 lysozyme, both strategies geared toward stabilizing the protein.In the end though, there is really no general strategy and that’s still the cardinal bottleneck; as the article's title says, a "trillion tiny tweaks" are necessary to make your system work. What works for one specific membrane protein fails for another. As one of the pioneers in the field, Raymond Stevens from Scripps says, “People are always asking what the one strategy that worked is. The answer is there wasn’t one strategy, there were about fifteen”. This is why chemistry (or economics) is not like physics. Although there are general rules, every specific case still invokes its own principles. In fields like membrane protein chemistry, it is unlikely that a single holy-grail strategy could be discovered that could work for all of them. The medley of techniques applied to membrane proteins makes the science seem sometimes like black magic and trial-and-error. All this makes chemistry hard, but also very interesting; if only a dozen membrane proteins have their structures solved, think of how many more are waiting in the shadows, awaiting the fruits of our sweat and toil.Baker, M. (2010). Making membrane proteins for structures: a trillion tiny tweaks Nature Methods, 7 (6), 429-434 DOI: 10.1038/nmeth0610-429... Read more »

Baker, M. (2010) Making membrane proteins for structures: a trillion tiny tweaks. Nature Methods, 7(6), 429-434. DOI: 10.1038/nmeth0610-429

September 12, 2010
08:10 PM
593 views

Did Comet Impacts Catalyze Amino Acid Production in Pre-Life Earth?

by Michael Long in Phased

Nir Goldman (Lawrence Livermore National Laboratory, United States) and coworkers' computer simulations suggest that the high temperatures and pressures of cometary impacts are sometimes within a range compatible with comets as a catalyst for amino acid synthesis in pre-life Earth. This news feature was written on September 12, 2010.... Read more »

Goldman, N., Reed, E. J., Fried, L. E., William Kuo, I.-F., & Maiti, A. (2010) Synthesis of glycine-containing complexes in impacts of comets on early Earth. Nature Chemistry. DOI: 10.1038/nchem.827

September 11, 2010
09:56 AM
1,143 views

Why modeling GPCRs is (still) hard

by The Curious Wavefunction in The Curious Wavefunction

Well, it's hard for several reasons which I have discussed in previous posts, but here's one reason demonstrated by a recent paper. In this paper they crystallized the ß2 adrenergic receptor with an antagonist. Previously, in the landmark publication of the ß2 structure in 2007, the protein had been crystallized with an inverse agonist. Recall that an inverse agonist inhibits the basal activity of the GPCR whereas an antagonist stabilizes both active and inactive states but does not affect the basal activity. In this case they crystallized the ß2 with an antagonist and compared the resulting structure to that of the agonist-GPCR complex. And they saw...nothing in particular. The protein backbone and side-chain locations are very similar for the antagonist (compound 3) and inverse agonist (compound 2) shown in the figure below. As we can see in the figure, about the only side-chain that shows any movement is the tyrosine on the left (Y316). No wonder that cross-docking the two ligands (that is, docking one ligand into the other ligand's protein conformation) gave very accurate ligand orientations; this was essentially a softball problem for a docking program since the antagonist was being docked into a protein conformation that was virtually identical to its own. But of course, we know that antagonists and agonists affect GPCR function quite differently. As this study shows, clearly the action is not taking place in the ligand-binding pocket where things aren't really moving. So where is the real action? It's naturally taking place on the intracellular side, where the GPCR interacts with a medley of other proteins. And as the paper accurately notes, the difference between antagonist and inverse agonist binding is probably also reflected in the protein dynamics corresponding to the two ligands. Good luck modeling that. That's the whole deal with modeling GPCRs. Simply modeling the ligand-binding pocket is not going to help us understand the differences between the binding of various ligands; one has to model multiprotein interactions and subtle effects on dynamics that are relayed through the helices. The program Desmond which I described in a earlier post is a powerful MD program, but even MD is going to really turn heads when it can take account of multiprotein interactions, and such interactions happen on a time-scale much longer than what even Desmond can access. We have a long way to go before we can do all this. But please, don't stop.Wacker, D., Fenalti, G., Brown, M., Katritch, V., Abagyan, R., Cherezov, V., & Stevens, R. (2010). Conserved Binding Mode of Human β-2 Adrenergic Receptor Inverse Agonists and Antagonist Revealed by X-ray Crystallography Journal of the American Chemical Society, 132 (33), 11443-11445 DOI: 10.1021/ja105108q... Read more »

Wacker, D., Fenalti, G., Brown, M., Katritch, V., Abagyan, R., Cherezov, V., & Stevens, R. (2010) Conserved Binding Mode of Human β Adrenergic Receptor Inverse Agonists and Antagonist Revealed by X-ray Crystallography . Journal of the American Chemical Society, 132(33), 11443-11445. DOI: 10.1021/ja105108q

September 10, 2010
05:40 PM
1,148 views

Spontaneous fermentation: the role of microorganisms in beer

by Katie Kline in EcoTone

Benjamin Franklin, one of the Founding Fathers of the United States, was once quoted as saying: “In wine there is wisdom, in beer there is Freedom, in water there is bacteria.” While there is certainly some truth to this quote, especially considering water quality in the 1700s, it should be noted that beer’s long history is also fraught with microorganisms—both helpful and harmful in the eyes of the brewer.

... Read more »

Sakamoto, K. (2003) Beer spoilage bacteria and hop resistance. International Journal of Food Microbiology, 89(2-3), 105-124. DOI: 10.1016/S0168-1605(03)00153-3

Nelson, M., Dinardo, A., Hochberg, J., & Armelagos, G. (2010) Brief communication: Mass spectroscopic characterization of tetracycline in the skeletal remains of an ancient population from Sudanese Nubia 350-550 CE. American Journal of Physical Anthropology. DOI: 10.1002/ajpa.21340

September 10, 2010
12:16 PM
1,288 views

In other news: self-regenerating solar cells

by Joerg Heber in All That Matters

This week my colleagues at Nature Chemistry landed an impressive scoop, the publication of a paper by Michael Strano and colleagues from MIT on self-regenerating solar cells. The performance of any kind of solar cell tends to degrade over time. This is particularly the case for organic solar cells, where sunlight can easily destroy the structure of the [...]... Read more »

Ham, M., Choi, J., Boghossian, A., Jeng, E., Graff, R., Heller, D., Chang, A., Mattis, A., Bayburt, T., Grinkova, Y.... (2010) Photoelectrochemical complexes for solar energy conversion that chemically and autonomously regenerate. Nature Chemistry. DOI: 10.1038/NCHEM.822

September 10, 2010
11:58 AM
1,179 views

Did Life Develop Shortly After Big Bang and Get Spread Throughout The Universe?

by Joseph Smidt in The Eternal Universe

I woke up to a very interesting paper by Gibson, Wickramasinghe, and Schild that appeared on the ArXiv last night and suggests that life most likely developed shortly after the big bang and was then spread throughout the universe. They call this the biological big bang. (And at this point I should say that universe here means the "local universe" that was in casual contact between 2-8 million

... Read more »

Carl H. Gibson, N. Chandra Wickramasinghe, & Rudolph E. Schild. (2010) First life in primordial-planet oceans: the biological big bang. Submitted to International Journal of Astrobiology. arXiv: 1009.1760v1

September 9, 2010
06:30 PM
558 views

Predicting Drug Tolerance via Biochemical Feedback Elucidation

by Michael Long in Phased

Peer Bork (European Molecular Biology Laboratory, Germany) and coworkers' computational analysis suggests that at least 8% of proteins are subject to drug-induced feedback loops, and therefore less susceptible to effective drug targeting. This news feature was written on September 9, 2010.... Read more »

Iskar, M., Campillos, M., Kuhn, M., Jensen, L. J., van Noort, V., & Bork, P. (2010) Drug-Induced Regulation of Target Expression. PLoS Computational Biology, 6(9). DOI: 10.1371/journal.pcbi.1000925

September 7, 2010
07:50 PM
433 views

Detecting Explosives with Nematodes

by Michael Long in Phased

Stephen Trowell (Commonwealth Scientific and Industrial Research Organization Entomology and Food Futures Flagship, Australia) and coworkers have shown that nematodes exhibit a selective positive chemotaxis response to airborne cyclohexanone, a solvent present in some explosives, in at least the low parts per million range. This news feature was written on September 7, 2010.... Read more »

Liao, C., Gock, A., Michie, M., Morton, B., Anderson, A., & Trowell, S. (2010) Behavioural and Genetic Evidence for C. elegans' Ability to Detect Volatile Chemicals Associated with Explosives. PLoS ONE, 5(9). DOI: 10.1371/journal.pone.0012615

September 7, 2010
11:00 AM
1,825 views

Chemistry of the Great Big Blue: Nutrients

by Bluegrass Blue Crab in Southern Fried Science

The Great Big Blue looks like it contains nothing but water and maybe a little salt, especially out in the open ocean. However, this kind of sparse environment is exactly where the chemistry matters the most – it’s a fine line between not enough, too much, and just right. Given this, there’s no distinct [...]... Read more »

HECKY, R., & KILHAM, P. (1988) Nutrient limitation of phytoplankton in freshwater and marine environments: A review of recent evidence on the effects of enrichment. Limnology and Oceanography, 33(4_part_2), 796-822. DOI: 10.4319/lo.1988.33.4_part_2.0796

Howarth, R. (1988) Nutrient Limitation of Net Primary Production in Marine Ecosystems. Annual Review of Ecology and Systematics, 19(1), 89-110. DOI: 10.1146/annurev.es.19.110188.000513

Behrenfeld, M., Bale, A., Kolber, Z., Aiken, J., & Falkowski, P. (1996) Confirmation of iron limitation of phytoplankton photosynthesis in the equatorial Pacific Ocean. Nature, 383(6600), 508-511. DOI: 10.1038/383508a0

Fanning, K. (1989) Influence of atmospheric pollution on nutrient limitation in the ocean. Nature, 339(6224), 460-463. DOI: 10.1038/339460a0

September 7, 2010
09:43 AM
509 views

How Plants Use Caterpillar Spit for Protection

by Steve W in Bridgehead Carbons

How do plants protect themselves from the bugs that chew on their leaves? In the case of the wild tobacco Nicotiana attenuata, when tobacco hornworm (manduca sexta) caterpillars feed on the leaves a collection of molecules called Green Leaf Volatiles (GLV's) is released by the plant. GLV's are released any time a leaf is damaged, but the interesting thing is that when the damage is done by chewing caterpillars, a different form of the GLV's are produced which attracts Big-Eyed Bugs (Geocoris spp) - a predator for the caterpillars.Image via WikipediaPlants emit two main types of volatile molecules: terpenoids and Green Leaf Volatiles. The terpenoids are emitted from the whole plant and usually after a delay - maybe as much as a day after the damage. The green leaf volatiles are more specific - they are emitted from the damaged leaf itself and it looks like they are produced at the same time as the damage.Green Leaf Volatiles are typically 6-carbon alcohols, aldehydes or esters. In the case of Nicotiana Attenuata they seem to mostly consist of hexenal, hexenol and simple esters of hexenol. The interesting bit is the alkene portion of these molecules. Alkenes can have one of two basic geometries around the double bond: the Z (or cis) isomer is locked into a u-turn shape and the E (or trans) isomer is locked into a zigzag-like orientation.Normally, Nicotiana attenuata produces mostly the Z isomer of these molecules and a relatively small amount of the E isomer. However something unusual happens when the damage is caused by caterpillars chewing on the leaves: in this case the plant produces roughly equal amounts of the Z isomer and the E isomer. You and I would probably not notice a difference in the smell of the leaves, but apparently there are bugs that can. When more E isomer is produced, more Big-Eyed Bugs are attracted to the plants. And the big-eyed bug eats caterpillars and their eggs. The E isomer GLV's are a plant distress call and the big-eyed bugs are the cavalry.How exactly does the plant "decide" which GLV isomers to make? After testing a variety of possible candidates, it looks as though there is an enzyme in the caterpillars' saliva that causes the Z isomers to isomerize to the corresponding E isomers. It is the caterpillar spit that produces the distress call.If you look closely at the Z molecules and the E molecules you will notice that there are actually two changes that take place. First, the geometry around the alkene switches. In general, the E isomer is more spread-out than the Z isomer and as a result it is lower in energy. Given a choice the alkene will usually adopt the E geometry. If there is a catalyst available, this change is pretty easy to understand.The second thing that changes is the location of the alkene, the alkene moves closer to the oxygen end of the molecule. Enzymes are very efficient molecules and they are very sensitive to shape. My guess is that the "real" target for the isomerase in the caterpillar saliva is the aldehyde. The aldehyde has a carbonyl group as well as the alkene and the most stable arrangement for these two functional groups is the one in hex-2-enal. When the two double bonds are separated by only one single bond their orbitals are able to interact and form a conjugated system. The conjugated version is more stable than the one where the two double bonds are farther apart and unable to interact with one another.If improved conjugation in the product is the reason that the alkene moves from the 3-position to the 2-position, why does the alkene move in the alcohol and ester molecules too? The alcohol has only one double bond since there is no C=O, so conjugation is not possible in this molecule. And while the ester does have a C=O, it is too far away to interact with the 2-alkene to form a conjugated system. What gives?Enzymes can be very selective about the molecules that they react with, but they can also be forgiving if the structure is not exactly correct. A lot of drugs affect specific enzymes in the body - the drug isn't exactly the correct shape, but it's close enough to bind to the enzyme. In the case of the GLV's, the alcohol and ester molecules are close enough to the right shape to bind to the enzyme and react. In the aldehyde the enzyme causes the alkene to migrate as well as change shape because it forms conjugated molecule. Even though the alcohol and ester don't benefit from forming a product molecule that has conjugation, the enzyme treats them the same way it treats the aldehyde and the alkene migrates to the 2-position.The other curious thing about this is the isomerase enzyme in the caterpillar saliva. I would bet the reason the caterpillars make this enzyme has nothing to do with attracting big-eyed bugs to come eat the caterpillars, that would be counter productive. The plants probably evolved their GLV's to take advantage of this enzyme that the caterpillars make anyway. So what is the isomerase "supposed" to do that benefits the caterpillars?The smell of freshly-cut grass is actually a plant distress call | IO9.COMAllmann S, & Baldwin IT (2010). Insects betray themselves in nature to predators by rapid isomerization of green leaf volatiles. Science (New York, N.Y.), 329 (5995), 1075-8 PMID: 20798319... Read more »

Allmann S, & Baldwin IT. (2010) Insects betray themselves in nature to predators by rapid isomerization of green leaf volatiles. Science (New York, N.Y.), 329(5995), 1075-8. PMID: 20798319

September 7, 2010
07:06 AM
697 views

What’s the buzz?: Synthetic marijuana, K2, Spice, JWH-018

by David J Kroll in Terra Sigillata

The topic of one of our most popular posts of all time has been the synthetic marijuana products containing JWH compounds, naphthoylindole cannabimimetics synthesized in the 1990s in the Clemson University laboratory of John Huffman. This post first appeared at the ScienceBlogs home of Terra Sigillata on 9 Feb 2010 and gives you some background [...]... Read more »

Aung MM, Griffin G, Huffman JW, Wu M, Keel C, Yang B, Showalter VM, Abood ME, & Martin BR. (2000) Influence of the N-1 alkyl chain length of cannabimimetic indoles upon CB(1) and CB(2) receptor binding. Drug and alcohol dependence, 60(2), 133-40. PMID: 10940540

September 5, 2010
01:45 PM
532 views

Antibiotic Resistance via Bacterial Charity

by Michael Long in Phased

James Collins (Boston University, United States) and coworkers have investigated the basis of antibiotic resistance from a communal perspective. This news feature was written on September 5, 2010.... Read more »

Lee H. H., Molla M. N., Cantor C. R., & Collins J. J. (2010) Bacterial charity work leads to population-wide resistance. Nature, 467(7311), 82-5. PMID: 20811456

September 3, 2010
10:43 AM
1,070 views

My E. coli brother's keeper

by The Curious Wavefunction in The Curious Wavefunction

Would an anti-indole work?Antibiotic resistance is one of the best examples of evolution in real-time and it’s also one of the most serious medical problems of our time. Emerging resistance in bacteria like MRSA threatens to bring on a wave of epidemics that may remind us of past, more unseemly times.Given the threat that antibiotic resistance poses, it is paramount to understand the mechanisms behind this process. While considerable progress has been made in understanding the genetic basis of mutations that confer antibiotic resistance, much less is known about the population dynamics of bacteria that evolve this kind of resistance. Now, in the cover story of the latest issue of Nature, researchers from Boston University discover a novel and remarkable mechanism by which bacteria acquire resistance. The mechanism is effectively a form of bacterial altruism.The researchers start by challenging successive generations of E. coli in a bioreactor with increasing concentrations of the antibiotic norfloxacin, which inhibits DNA synthesis by binding to DNA gyrase. Around the tenth generation or so, they notice something interesting. Not all bacteria have evolved resistance to the antibiotic, but there’s a very small population of bacteria with high resistance. However, in the next few generations, the other bacteria also seem to acquire this resistance. What’s going on?It turns out that the small populations of bacteria which are highly resistant are actually ‘teaching’ their fellow bacteria to become resistant. They are doing this by a remarkably simple mechanism- by secreting the molecule indole into their environment. This indole acts as a signaling molecule that is mopped up by the other bacteria. The result is the activation of a variety of resistance mechanisms, including increased production of drug transporter proteins which are well-known to confer resistance by extruding drug molecules out.Now indole is well-known as a component of signaling molecules. For instance, indole-3-acetic acid (IAA) plays many important signaling roles in plants and encourages cell growth and division. The detection of indole by itself was not surprising in this case, since all the bacteria secreted indole as part of their regular metabolism in the beginning. But what was surprising was the mechanism; as the antibiotic stressed out the bacteria, most of them essentially weakened and stopped indole-secretion with the exception of this small cadre of selfless individuals who kept on generating the molecular signal. Since production of indole in times of stress clearly requires an investment of energy, this was a bona fide case of bacterial altruism; sacrifice one’s own fitness to increase that of the group.Ultimately though, we don’t want to just understand such novel mechanisms of antibiotic resistance but want to thwart them. Based on this mechanism I had an idea. If indole is so important for bacteria to acquire resistance, then one logical way to counter resistance would be to introduce an ‘anti-indole’ in their environment and mix it up with the natural molecule to cause confusion. This anti-indole would be a molecule resembling indole- an indole mimic and antagonist- that would effectively compete with indole for uptake, without causing any of the resulting effects. Most likely this molecule would be a very close analog of indole, perhaps indole with a hydroxyl or fluoro group on it. Any small modification of indole would do, as long as it’s enough to confuse the bacteria. Of course we would also need to worry about bioavailability and toxicity, but I don’t see why the basic strategy would be completely unfeasible and why a proof-of-principle experiment could not be done in a petri dish.Lee HH, Molla MN, Cantor CR, & Collins JJ (2010). Bacterial charity work leads to population-wide resistance. Nature, 467 (7311), 82-5 PMID: 20811456... Read more »

Lee HH, Molla MN, Cantor CR, & Collins JJ. (2010) Bacterial charity work leads to population-wide resistance. Nature, 467(7311), 82-5. PMID: 20811456

August 31, 2010
07:00 AM
1,770 views

Chemistry of the Great Big Blue: Metals

by Bluegrass Blue Crab in Southern Fried Science

The ocean is full of metals and minerals that naturally occur such as zinc, copper, and cobalt and many marine organisms therefore depend upon access to those metals in small concentrations. However, inshore marine systems receive inputs from industrial, mining, and stormwater runoff that far exceed what these organisms can use. So what’s the effect? [...]... Read more »

M. Mayer-Pinto, A.J. Underwood, T. Tolhurst, R.A. Coleman. (2010) Effects of metals on aquatic assemblages: What do we really know?. J. Exp. Mar. Biol. Ecol., 1-9. info:/

August 30, 2010
10:05 PM
537 views

All Thirteen Priority Elemental Pollutants Emitted via Oil Sand Extraction

by Michael Long in Phased

David Schindler (University of Alberta, Canada) and coworkers have thoroughly destroyed the claim that oil sand extraction, as currently practiced, is safe for the environment. This news feature was written on August 30, 2010.... Read more »

Kellya, E. N., Schindlera, D. W., Hodsonb, P. V., Shortc, J. W., Radmanovicha, R., & Nielsena, C. C. (2010) Oil sands development contributes elements toxic at low concentrations to the Athabasca River and its tributaries. Proceedings of the National Academy of Sciences. info:/10.1073/pnas.1008754107

August 30, 2010
05:38 PM
587 views

Assessing computationally designed enzymes

by The Curious Wavefunction in The Curious Wavefunction

One of the most promising recent developments in computational biochemistry is the development of potential capability to design entirely new enzymes that can perform reactions inaccessible to naturally occurring proteins. Such enzymes can be of great utility as novel biofuels, synthetic reagents and new drugs. A particularly noteworthy set of publications in this regard were from David Baker’s and Ken Houk’s groups in Seattle and Los Angeles. In 2008, the groups designed an enzyme for performing a Kemp elimination reaction. A couple of months back, they again made news by designing a Diels-Alderase from scratch, an enzyme catalyzing the DA reaction whose natural counterpart does not exist. Although the catalytic rates they obtained were relatively modest compared to the best rates seen in nature, this is still an important and remarkable step forward.The studies hinged on two tools- quantum mechanical design of a transition state for the enzymatic reaction, and buildup of the protein architecture around this ideal transition state using the program Rosetta. In the first step, a transition state for the reaction was surrounded by specific amino acid residues and optimized in an ideal geometry. This arrangement is called a “theozyme”, an ideal, minimal theoretical construct. In the second step, Rosetta was used to ‘embed’ this theozyme in a protein framework borrowed from existing protein structures in the PDB. Iterative cycles of optimization of the amino acids around the reactants led to several designs. Some of these designs turned out to be active, and crystal structures revealed the remarkable similarity between the computer and real-life counterparts. However, there was no easy way except actual testing to distinguish active and inactive designs beforehand (the inactive designs could not be crystallized since by definition they were probably too unstable to form crystals).Now a new analysis nicely looks at the difference between the active and inactive designs obtained for the Kemp elimination. The authors first try to use static quantum chemistry calculations to resolve the difference between the two sets. Unfortunately this does not work very well since the energy difference between the sets are quite small, about 2 kcal/mol, and QM methods for such complex systems can often produce comparable errors.However, enzymes are dynamic creatures, and it’s probably not too surprising that one has to resort to dynamical studies to discern the differences between active and inactive structures. To this end, the authors used 20 ns MD simulations. They compared the results with two designed Kemp eliminators (including one antibody) whose crystal structures are available. Firstly, they simply observed the mobility of the residues in the active sites and found out that in general, residues in the active designs don’t move around as much as those in the inactive ones, indicating stable packing. Then they looked at the hydrogen bonds holding the reactants together. In general, they found a tighter distribution of hydrogen bond angles in the active and crystallized structures compared to the inactive ones. This observation would be in keeping in line with the optimized hydrogen bonding networks in active sites. Lastly, they looked at accessibility of water in the active site. The base involved in the Kemp elimination is a carboxylate. Ideally, this carboxylate would not be solvated so that it is free to serve as a base. Indeed, analysis of water molecules surrounding this carboxylate indicated that while the carboxylates in the active, crystallized proteins are almost completely free of water molecules, the carboxylates in the inactive designs are typically surrounded by a couple of water molecules. This also again confirms the ‘looser’ packing in the inactive sites.This is a nice study because it not only validated MD as a possible tool to distinguish and rank active and inactive designed enzymes, but it also provides insights into the basic physical features of optimized enzyme sites. Compact, packed side-chains, optimal hydrogen bonding geometries and relative inaccessibility of key residues to water is about what you would expect Nature to do when ‘designing’ enzyme active sites.Kiss, G., Röthlisberger, D., Baker, D., & Houk, K. (2010). Evaluation and ranking of enzyme designs Protein Science DOI: 10.1002/pro.462... Read more »

Kiss, G., Röthlisberger, D., Baker, D., & Houk, K. (2010) Evaluation and ranking of enzyme designs. Protein Science. DOI: 10.1002/pro.462

August 23, 2010
09:05 PM
529 views

A Web Server for Identifying the "Hot Spot" of Protein-Protein Interfaces

by Michael Long in Phased

Narcis Fernandez-Fuentes (University of Leeds, United Kingdom) and coworkers' web server will greatly accelerate the development of drugs which target protein-protein interfaces. This news feature was written on August 23, 2010.... Read more »

Segura Mora, J. S., Assi, S. A., & Fernandez-Fuentes, N. (2010) Presaging Critical Residues in Protein interfaces-Web Server (PCRPi-W): A Web Server to Chart Hot Spots in Protein Interfaces. PLoS ONE, 5(8). DOI: 10.1371/journal.pone.0012352

August 22, 2010
12:30 AM
771 views

Of blood and breath: metabolite-based diagnosis of ovarian cancer

by Aurametrix team in Olfactics and Diagnostics

Physicians always knew that breath contains clues to diseases. Chemicals in breath often correlate with chemicals in saliva and blood - be it alcohol, anaesthetics or other metabolites (see, for example, this study by Dr Andreas Hengstenberg).As one of my interests is breath-based detection of ovarian cancer, I took note of the recent paper claiming 99% to 100% accuracy of detecting ovarian cancer by metabolites in blood. The authors used customized functional support vector machine-based machine-learning algorithms to classify thousands of metabolites measured by mass spectrometry (JEOL AccuTOF™ DART® that allowed to forego conventional liquid chromatography as sufficient resolution was achieved without separation) in peripheral blood. 100% sensitivity and 100% specificity was achieved with 64-30 split validation technique, while 100% sensitivity and 98% specificity was the accuracy of leave-one-out-cross-validation. Very large number of metabolites, from 2,000 to 3,000 features, contributed to such discriminatory power (see the list of 14,000+ in supplemental material) Set of 25 canonical metabolic pathways relevant to the uploaded elementalformulae ranked according to their p-values (hypergeometric distribution).Histamine, amino acid, fructose and glucose metabolism were among the most prominent processes discriminating cancer and healthy blood. It's that simple: sugar feeds cancer. Scientists have long found that cancer cells slurp fructose, and that fructose intake can be linked to some cancers. Histamine/polyamine interplay in cancers is also known. Histamine may be involved in inhibition of the local immune response against cancer. Is amino acid metabolism also linked to cancer? Well, what is not. Metabolomic biomarkers were always known to have diagnostic potential - cholesterol and glucose are among the oldest and most widely performed diagnostic tests. Yet, most bleeding edge cancer detection platforms are genomic or proteomic in nature. Of the thousands of known biomarkers, only a handful have made it into the clinic. Existing ovarian cancer tests mostly rely on detecting a protein - carbohydrate antigen 125. Vermillion's OVA1 and HealthLinx OvPlex tests use five proteins. This may be extended to 7.Metabolites represent the end products of the genome and proteome, thus metabolomics-based diagnostics holds the promise of providing powerful diagnostics, allowing for differentiation of increased and decreased levels of chemicals with low process coefficient of variation. Metabolomic tests were used for medical diagnostics starting with Hippocrates and Lavoisier. They continue to be explored by modern scientists. Dr Michael Phillips, for example, developed HeartsBreath Test, approved by the US Food and Drug Agency for early diagnosis of heart transplant rejection. Research proved the potential of inexpensive breath tests in discriminating lung, breast, colon and prostate cancers. Let's hope the new article - along with others - will lead to novel consumer products, not only more academic research and peer-reviewed publications.Zhou M, Guan W, Walker LD, Mezencev R, Benigno BB, Gray A, Fernández FM, & McDonald JF (2010). Rapid Mass Spectrometric Metabolic Profiling of Blood Sera Detects Ovarian Cancer with High Accuracy. Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology PMID: 20699376... Read more »

Zhou M, Guan W, Walker LD, Mezencev R, Benigno BB, Gray A, Fernández FM, & McDonald JF. (2010) Rapid Mass Spectrometric Metabolic Profiling of Blood Sera Detects Ovarian Cancer with High Accuracy. Cancer epidemiology, biomarkers . PMID: 20699376

August 20, 2010
01:40 PM
1,985 views

Cylons and Smelloscopes: False Positives and False Negatives in the Search for Extraterrestrial Life

by The Astronomist in The Astronomist.

Are there planets outside of our solar system? Is there life on other planets? Is life on other planets like life on Earth? These are questions that astronomers, astrobiologists, chemists, and geologists are trying to answer with current experiments. In order to answer these questions we must observe distant planets and we must determine what life on those planets may be like. Detecting extrasolar planets is tricky enough, but imaging what alien life is like may well be stranger than science fiction. Yesterday evening I attended a lecture sponsored by the Seattle Astronomical Society given by Shawn Domagal-Goldman titled Cylons and Smelloscopes: False Positives and False Negatives in the Search for Extraterrestrial Life. It was an excellent lecture and filled with interesting topics. Shawn touched on the philosophical problem of defining life in the broadest of senses (is Number Six alive?) and he pointed out that the verification of life on distant planets faces technical challenges and basic scientific limitations (a smelloscope sure would help!).Dimitar Sasselov set off minor shock waves of gossip and rumors in the media and astronomy communities when claimed that the NASA Kepler mission had found 140 Earth-like planets a few weeks ago during a talk he gave at the TED Global 2010 meeting in Oxford. The media thought we had found earth's twin, but astronomers knew that Sasselov had exaggerated the situation. Sasselov had to post a redaction of sorts on the Kepler blog in order to clarify what he said. What he should have said is that the Kepler mission will find and verify the presence of potentially habitable planets and that Kepler currently had 140 candidate extrasolar planets. The candidates are not confirmed and so a pessimistic outcome could be that half of the candidates will be false. The difficulty in finding extrasolar planets or life is fraught with false positive and false negatives. A false positive is a detection that seems like exactly what you were looking for, and maybe it is, but the detection was either bad data or you were looking for the wrong thing. A false negative is a detection which you conclude is not what you were looking for, but either your data was fouled or your detection threshold was too constrictive.How do we find planets outside of our solar system? There are at least five methods to find planets: Doppler shift, astrometric measurement, transit method, gravitational microlensing, and direct detection. Shawn discussed in depth the Kepler mission that is currently monitoring more than 150,000 stars in the direction of the Cygnus constellation for any signs of extrasolar planets that may be orbiting those stars. So, what method does Kepler use to find planets? It watches for eclipses! When a planet orbiting a distant star crosses in front of the star some of the light from the host star is blocked. The planet will transit (astronomers often use the world transit not eclipse for exoplanets) in front of the the star once an orbit and thus the period of orbit can be determined. A secondary eclipse also occurs when the day side of the planet is blocked by the star. The video below illustrates the whole process.Yes, there are planets outside of our solar system. The current exoplanet detection count is 473 and counting; you can watch that count go up over at Planet Quest. Kepler may double that number, but more importantly it has the ability to find earth size planets. Most of the planets found to date have been large, hot, and inhospitable to most kinds of life anyone can fathom. How do we detect signs of life on other planets? Astronomers look for bio-markers in the planet's atmosphere. Bio-markers are molecular signatures of certain compounds that could not be produced by non-biological process; bio-markers indicate that dynamic non-equilibrium chemistry is present on the surface of that planet. Astronomers can measure the light emitted as a function of wavelength, the spectra, that a planet emits to determine the molecular species present in the atmosphere. For example the Earth's atmosphere has the spectral signature of water which means it has conditions in which life as we know it can thrive. If we found an earth size planet that had water in its atmosphere which wasn't too hot we would say we had found a habitable planet. If we found oxygen or ozone (03) in an atmosphere it would almost certainly mean life was present on the planet because 03 is quickly removed from atmospheres through standard geological processes such as oxidation of iron, but it may remain present in an atmosphere if it is continually replenished by the photosynthesis mechanism of algae and plants. One of the topics Shawn talked about in his talk and a focus of his research was the problem of being certain that non-biological processes are not creating the oxygen rich atmospheres. The runaway greenhouse effect combined with the photo-disassociation of carbon dioxide can produce oxygen in a similar way to biological life. This is where the smelloscope would be useful: ozone along with other non-equilibrium species such as nitrous oxide and methane in specific ratios would be the scent we are looking for. Bio-signatures were not present on the early Earth. In fact the Earth probably looked a lot more like Venus. The diagram above shows that Venus, Earth, and Mars all have distinct spectral features that tell us about their atmospheres. The hardest part of looking for bio-signatures is that we do not have a telescope that is sensitive enough. Trying to take the spectra of a planet orbiting a bright star is like trying to tell the color of the wings on a gnat hovering around a spotlight on the moon. Like a baseball player holding up one hand to block the sun from his eyes as he focuses on the ball an occulter or star shade working with an existing telescope in space would do the trick. The current funding situation in astronomy is dire, but there is hope that a mission called New Worlds will one day work with the James Webb Space Telescope to allow us to take a closer look at planets which Kepler is finding.Is there life on other planets? We don't know and it may be a more complicated question than is suspected. There is a bias towards looking for life that is similar to what life on Earth is like. There is a bias towards looking for life that alters its host planet's atmosphere significantly enough to detect it with telescopes on earth. There is a bias towards looking for life that is alive as we define it. These biases may lead to false negatives in the search for life, but as Shawn pointed out the possibilities for life to exist are much grander than our imaginations so we do the best we can. Also, despite the difficulties for finding life on other planets and the gulf between the public's perception of aliens and reality scientists are taking this as a serious venture. Scientists from diverse fields are coming together to forge a path forward. One such project is the Virtual Planet Laboratory which employs scientists in fields such as geology, chemistry, biology, and astronomy. The Virtual Planet Laboratory is a team of scientists who are building computer simulated planets to discover the likely range of planetary environments for planets around other stars so we can better look for habitable planets and distinguish between planets with and without life. However, we can't even discern with certainty the presence of life on Mars or Europa at this point, what hope do we have for finding life on distant planets?I think there is a lot of hope and I am not alone in that sentiment. I don't search for planets or life in my research, but I think that the search for life, pa... Read more »

Beichman, C. A., Woolf, N. J., & Lindensmith, C. A. (1999) The Terrestrial Planet Finder (TPF) : a NASA Origins Program to search for habitable planets. JPL publication. info:/

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