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 ...


8

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 ...


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 ...


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

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

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 ...


5

The authors mention three residues that they consider "second shell", 12, 77, and 102. They are shown in the figure below in green: Residues Trp50 and Glu101 are directly involved in ligand binding, shown as space-filling in yellow. As you can see, they are part of the central beta barrel. The residues in green are also part of the beta barrel, but the side ...


4

Chemical formulas of the type you describe are just as valid for large molecules as for small ones. The reason they are not commonly used is that the number of possible molecules described by a given formula goes up exponentially with the number of atoms. Thus, it is much more common to describe larger molecules with more precise terms. In the case of ...


4

What you've described is the field of electronic structure theory. To obtain the electronic density from the cartesian coordinates of the atoms requires immense amount of computation (assuming you have a protein in your pdb file). If you have a small molecule, you could use any number of common electronic structure packages. ORCA is open-source (assuming ...


3

This nomenclature is due to the fact that amino acids are carboxylic acids. Near the carboxylic acid moiety, the carbon chain is unbranched and simple, so the positions are named like an unbranched, simple aliphatic carboxylic acid. The carboxylic acid ($\ce{-CO2H}$) is not indicated with a position. But the carbon immediately next to it is $\alpha$. The ...


3

Given your hypothesis that the three $\mathrm{p}K_\mathrm{a}$'s are dependent on one another and that experimentally you do not seem to be able to identify which histidines are protonated and which are not at any given time, it would seem that the simplest model to use is that of a triprotic acid such as citric acid. The triple HH equation model you used is ...


3

Acetylcholinesterase is important enzyme and its mechanism of function is well known. In active site, it has two pockets: anionic pocket (to attract positively charged Quaternary nitrogen of choline) and esteric pocket. The esteric pocket consists of a serine side chain (a $\ce{-CH2-OH}$ function) as depicted in following cartoon, which pacilitate the ...


3

The good mnemonic tool to remember is : Anode = anabasis, electrons would be going upwards from the electrode to the wire = oxidation, ( Xenophon, Anabasis, 404BC, "The journey upwards(to north)) Cathode = cathabasis(the journey downwards), electrons would be going downwards from the wire to the electrode = reduction That means a cathode/anode is the ...


2

You can conveniently normalize the peak height to unity, if your sole purpose is to compare the peak shapes. It is not forbidden at all. However you should not attempt any quantitation. You can read the paper here Total peak shape analysis: detection and quantitation of concurrent fronting, tailing, and their effect on asymmetry measurements


2

I assume you have a UV/Vis absorbance based measurement. Then the absorbance should follow Beer´s Law which states that absorbance is proportional to concentration. Therefore you should be fine with your normalization approach. You could check if you are in the linear range by performing a calibration.


2

This is a great introduction to the concept of lack of precision (ie error) in measurements. It is unlikely that your volumes are exactly 5 mL and 6 mL or that your protein concentrations are exactly 20 mg/mL and 18 mg/mL. The errors in these measurements combine to give different calculated protein amounts even though the protein amounts are presumably the ...


2

If we call the drug L, and the binding sites S, the equilibrium is the following: $$\ce{LS <=> L + S}$$ The equilibrium constant expression is: $$K_d = \frac{[\ce{L}] [\ce{S}]}{[\ce{LS}]}$$ With $[\ce{L}]_\mathrm{tot}$ as the total concentration of ligand and $[\ce{S}]_\mathrm{tot}$ the total concentration of binding sites, we can solve of $[\ce{L}]...


2

Regarding the second question, post-translational modification is not the only way. https://en.wikipedia.org/wiki/Isopeptide_bond, and the references therein, answer your questions quite nicely. These are relatively uncommon (compared to the usual peptide bond) because enzymes are capable of exerting control over which carboxylic acid / amine reacts: you ...


2

Dynamics can mean many things, and not all proteins undergo extensive conformational changes during their lifetime. Some are fairly rigid in solution. XRD or NMR data represents an average over the conformations of a protein construct sampled under experimental conditions. A protein construct is a variant of the protein, selected to allow expression and ...


2

Until the late 2010s, it was considered impossible to reactivate acetylcholinesterase that has undergone aging. However, in recent years, new advancements have been made that show promise in this area. A group of researchers investigated several sulfonium-containing alkylating agents that were supposed to alkylate the phosphonate moiety bound to the serine ...


2

Question 1: Why is that one(in space) considered alpha and not the carbon atom next to it? All human proteins consist of $\alpha$-amino acid residues. An $\alpha$-amino acid means the carboxylic acid group ($\ce{COOH}$) and amino group ($\ce{NH2}$) are separated by one $\ce{C}$ carbom atom, which is called $\alpha$-carbon ($\ce{C}_\alpha$; See the insert at ...


2

From the abstract of the article in question: The results suggest that the pressure stability of a protein in solution is not directly affected by the presence of these proposed piezolytes, and so they cannot be granted this distinction. So the answer is "no", the supposed piezolytes do not appear to have the purported function. They do stabilize ...


1

Matthew's answer corrected some mistakes which I have made in asking my question. His answer also suggests that OP compounds that contain hydroxyl groups would indeed cause instant aging of inhibited cholinesterase. I have found confirmation that that is indeed the case. There is a naturally-occurring organophosphate that contains a hydroxyl group, formerly ...


1

In this report, diaminopropane is used to elute a lectin from an affinity column. They mention the pH, which is the key to the question. The bound lectin was eluted with 20 mM diaminopropane containing 0.15M NaCl, pH ~11. The diaminopropane is unbuffered, and the high pH weakens the interactions between lectin and carbohydrates.


1

If all fractions contain the same protein, I'd combined all and concentrated the combined solutions to desired concentration using biochemical techniques such as dialysis. If they contained more than one protein, then I'd combined all fraction collected under the correct peak. However, it is better ask your supervisor (or adviser) before you combined them. ...


1

To expand on Mithoron's comment, it's absolutely necessary to equilibrate (or at least minimize the energy) of your system once you've introduced an appreciable perturbation of any sort (in this case, you've appreciably changed the system itself!). To give you an idea, some lesser changes that would still justify equilibration are: changes in solvation, ...


1

The difference between a monomer and a protomer depends on the associations of the molecule and its 3D structure. A monomer is the isolated unit molecular component (i.e. free or soluble form) of a potential oligomer or polymer. A protomer is the molecule after a conformational change into the shape it takes when incorporated as part of that oligomer or ...


1

Lacking an answer for 3 years, I'm going to attempt to answer this based on internet definitions and logic. Please, I welcome any insight from chemistry experts to improve this answer. First of all, the Wikipedia link quoted actually gives two definitions for protomer. The one quoted is the "structural biology" definition rather than the "chemistry" ...


1

Your question is about immobilized metal affinity chromatography (IMAC), often used to separate a protein expressed in the E. coli bacterium from other proteins made by it. The protein of interest is expressed with a histidine-containing affinity tag which binds to immobilized nickel or cobalt at neutral or basic pH. Immobilization is achieved by complexing ...


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