# Tag Info

27

Cyanide is a pretty good ligand for coordination compounds. The electron pair on carbon (which, incidentally, also carries the Lewis structure’s formal charge) is located in the HOMO — much like as in $\ce{CO}$, whose molecular orbitals can be found in this answer by Martin (replace oxygen with nitrogen to arrive at $\ce{CN-}$) — making it a good Lewis base ...

19

It doesn't make calcium carbonate rubbery, it removes the calcium carbonate. Egg shells are not purely calcium carbonate they are more like a composite with a continuous matrix of calcium carbonate and a smaller continuous matrix of protien. When you put the egg in vinegar, you etch away this calcium carbonate matrix leaving the formerly less noticeable ...

18

An eggshell is a complex structure. From Wikipedia: Boiling the egg removes the waxy cuticle from the outside of the egg, dissolves a small but not insignificant amount of calcium carbonate from the shell, damages the protein matrix that holds calcium carbonate crystals in place in the shell, and can disrupt or destroy the two shell membranes. All of ...

10

Imagine an infantry unit of soldiers marching in file. Each of them may be quite irregular, but together they form a repeating pattern. And that's exactly what happens with protein molecules in a crystal. When we say that a protein is irregular, we mean it on a different level. Indeed, one molecule of our protein is irregular if we are talking about the ...

10

The phosphoric acid causes denaturation of milk proteins which precipitate out of the solution (milk is an emulsion, to be exact). The flock that is formed also adsorbs dye molecules (caramel) which is why the solution become clear. There is nothing coke-specific about it. Any acid would denature milk just like that. And nearly any huge organic molecule ...

10

TL;DR: It is not really "one or the other" - it is more of "somewhere in between", like a resonance hybrid. If I had to choose, I'd personally lean towards Weiss's $\ce{Fe(III)-O2-}$ model. However, there will always be people who disagree, and there is still no general consensus amongst the scientific community. There is an excellent - and recent - ...

10

Are you asking how to take code developed to find the MFE (minimum free energy) structure of a single protein, and modify it to instead determine the structure of a two-protein complex? Or are you asking if you can use this code, as is, to fold a concatenated combination of the two proteins, and in turn use this result as a surrogate for the predicted ...

9

There's several aspects to your question. Does quantum mechanics play a role in protein folding? Yes. The origin of the van der Waals interaction is ultimately a quantum mechanical one. (At least the induced dipole portions: how the electrons move with respect to each other and an external electrical field is driven by quantum mechanics.) Also, while part ...

9

Szilágyi and Závodszky published an article in the journal Structure which analyses a number of different structural parameters of proteins of moderately thermophilic ($45~\mathrm{^\circ C} < \vartheta_\mathrm{opt} < 80~\mathrm{^\circ C}$) and hyperthermophilic ($\vartheta_\mathrm{opt} \approx 100~\mathrm{^\circ C}$) organisms compared to homologous ...

9

There is a clear explanation and figure showing this in the following reference: Anton Gorkovskiy, Kent R. Thurber, Robert Tycko, Reed B. Wickner, PNAS 2014, 111 (43) E4615-E4622. A parallel beta sheet is one where the direction from N- to C-termini on adjacent strands run in a parallel direction (rather than antiparallel). In-register means that each ...

9

That is because the solution to the structure isn't done just via the plate. The signal you see on the plate is what is called "structure factors" of the experiment. They are associated with the fourier transform of the electron density. There are computational ways of obtaining the electron densiy once you have the structure factors. When you do ...

8

Typically crystal structures are determined by X-ray diffraction off of electrons within a bond and around the nuclei of each atom. Since H only has 1 electron, and its often involved in a polar type bond (hence doesn't spend much time by the H nucleus when bonded) it is notoriously hard to "see" with X-rays. In order to have X-rays diffract accurately off ...

8

Ivan basically gave a nice and clear example of what is going in. I’m going to offer a more in-depth explanation. If you were to consider possible crystal structures of just one type of atom, you can boil the possible structures down to a set of similar structures, the Bravais lattices. Only 14 of these exist with different constraints: i.e. the C-centred ...

8

Equilibrium in aqueous solution In aqueous solution (such as our digestive tract), the equilibrium of the reaction as written is on the side of the reactants. Digestive enzymes catalyze the hydrolysis of peptide bonds, showing that they are not thermodynamically stable in water. However, in the absence of catalysts at neutral $\mathrm{pH}$, the peptide bond ...

7

Most of the structures in the Protein Databank are determined with X-ray crystallography. Like inorganic compounds and small organic molecules, under the right conditions proteins can form crystals - ordered, repeating patterns of protein molecules, filling a 3D space. That is, you can take a basic building block and rotate and translate this building block ...

7

This is a bit more complicated than it seems. Milk contains about 3% protein. Most proteins are not soluble -- otherwise our bodies would dissolve when it rained! The most common type that are soluble are the albumins, which rely on their tertiary structure for solubility. Hence anything that disrupts the tertiary structure -- denatures it -- can expose ...

7

I don’t think you are wrong. Actually molecular chaperones have been named enzymes in some texts. The molecular chaperones comprise several unrelated classes of proteins that have rather different functions. Most molecular chaperones are ATPases (enzymes that catalyze ATP hydrolysis), which bind to unfolded polypeptides and apply the free energy of ...

7

Yes, the arginine side chain is an excellent hydrogen bond donor. Charged N-H groups are even better hydrogen bond donors than the corresponding neutral N-H groups. Here is an article that gives examples of arginine side chains in hydrogen bonds. It showcases bidendate hydrogen bonds (i.e. two hydrogen bonds from the arginine side chain) with carboxylates ...

7

It is far, far more difficult that a naive approach suggests The reason why simulating protein folding is extremely hard is the combinatorial complexity of the options you have to explore to get the "right" answer. This exhausts your computers memory or computing capacity far faster than it will for simple molecules. It is possible to see why this ...

6

Protein folding takes a very long time (relatively speaking) when thinking of quantum mechanical effect. First note that, in principle, for the time being, quantum mechanics is considered to be universally valid at all size and time scales. So, in general, it does not really matter how big a system is or how long a process takes: every system is a quantum ...

6

I'll use quotes from B. Rupp, Biomolecular Crystallography (p. 7-8) to answer. Generally the structure is similar... Comparison of many nuclear magnetic resonance (NMR) solution structure ensembles with crystallographic structure has shown that the core structure of protein molecules remains unchanged compared with the solution state during ...

6

if you cap then you “block” all of the peptides that you are synthesizing.(?) No, you don’t, the order of steps is important. First you try to couple your new amino acid to the solid phase. You will end up with uncoupled ends with free amino groups and coupled ends with a protected amino group. Then you cap, e.g. with phenoxyacetic acid anhydride. This will ...

6

The premise of this question is based upon outdated information. According to Study: Novel botulinum toxin less dangerous than thought Researchers from the Centers for Disease Control and Prevention (CDC) and the University of Wisconsin (UW), writing in the Journal of Infectious Diseases (JID), said it turns out that the novel toxin can be blocked by ...

6

Some parts a the protein are a bit more flexible, also in the protein crystal. These parts don't give clear electron density after x-ray diffraction, and are removed from the resulting model structure. Often the N- and C-terminal ends are removed, this is something you'll find in many .pdb structures, but sometimes also loops are removed, resulting in two ...

6

Pretty hard question, "why", as we've not been watching for the millions of years it took to build that system... I think the better way to look at it is to name the advantages this system has and hypothesize on it's selection. BTW in biology a good answer to why is always because. I would guess though that given the function of ligases, it has been ...

6

Chitin and protein are completely unrelated. The only common thing is that they are polymers. Chitin is a polymer of amino sugars while protein is a polymer of amino acids. Both monomers are very different and are not converted one to the other. In fact, chitin, like cellulose, is not fragmented by animals, so it is not absorbed. Moreover, chitin is a ...

6

Who was responsible for this naming system and how can we change it? Michael Faraday was responsible for the terms anode and cathode more than hundred years ago. All the confusion regarding the nomenclature will vanish if you do not associate electrostatic signs with these two terms. One should identify the electrode labels with the redox processes rather ...

6

If you got an installation of openbabel's GUI, you equally have an installation of openbabel for the terminal (e.g., in Linuxes) / command line cmd.exe (in Windows). There is nothing wrong using the GUI for an edit on one file or a few data -- your instructions set are right -- however using the CLI is closer to the engine, thus often more powerful. Enter ...

6

For the more recent structures, you can view the density (based on measured diffraction data and the model, so-called 2Fo-Fc density) directly in the protein data bank, e.g. http://www.rcsb.org/3d-view/6QU9?preset=electronDensityMaps: For a theoretical model or a model without deposited diffraction data, you would first have to generate structure factors, ...

6

In short: Joining amino acids to build proteins does not just assemble rigid bodies together. Maybe you think it is joining a carboxylic acid and an amine to form an amide and to identify a conformation corresponding to the global energetic minimum around this unit. It surly was not this easy to enter successfully CASP14. Without intent to list all ...

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